diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index f49cfb3a..e59f1aef 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -1,2 +1,3 @@ # Autoformat all files using `black` 8f061e7da99eb78353e9392d6929673da5b352a3 +91078a63c64ec9a1c2de7f72a835813b888d1c73 diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 54830999..820a9521 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -26,33 +26,33 @@ jobs: strategy: fail-fast: false matrix: - # only test all GROMACS version on the oldest and latest - # Python to keep the testing matrix manageable and only use 2 - # macos runners (latest GROMACS, oldest and latest Python) + # only test all GROMACS version on the latest + # Python to keep the testing matrix manageable and only use 1 + # macos runners (latest GROMACS, latest Python) os: [ubuntu-latest] - python-version: ["3.10"] - gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1", "2022.4", "2023.1"] + python-version: ["3.12"] + gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1", "2022.4", "2023.1", "2024.3"] include: - os: ubuntu-latest - python-version: "3.8" - gromacs-version: "2023.1" + python-version: "3.10" + gromacs-version: "2024.3" - os: ubuntu-latest - python-version: "3.9" - gromacs-version: "2023.1" + python-version: "3.11" + gromacs-version: "2024.3" - os: macos-latest - python-version: "3.10" - gromacs-version: "2023.1" + python-version: "3.12" + gromacs-version: "2024.3" env: MPLBACKEND: agg steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: mamba environment and package installation - uses: mamba-org/setup-micromamba@v1 + uses: mamba-org/setup-micromamba@v2 with: environment-file: devtools/conda-envs/test_env.yaml condarc: | @@ -93,7 +93,7 @@ jobs: pytest -v --durations=20 --cov=mdpow --cov-report=xml --color=yes ./mdpow/tests - name: Codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml new file mode 100644 index 00000000..2cc9d7fc --- /dev/null +++ b/.github/workflows/deploy.yaml @@ -0,0 +1,57 @@ +name: Build and upload to PyPi + +on: + push: + tags: + - "*" + release: + types: + - published + +jobs: + test_pypi_push: + environment: + name: TestPyPi + url: https://test.pypi.org/p/MDPOW + permissions: + id-token: write + if: | + github.repository == 'Becksteinlab/MDPOW' && + (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')) + name: "TestPyPi: Build and upload pure Python wheels" + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: testpypi_deploy + uses: MDAnalysis/pypi-deployment@main + if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') + with: + test_submission: true + package_name: 'MDPOW' + module_name: 'mdpow' + tests: false + + pypi_push: + environment: + name: PyPi + url: https://pypi.org/p/MDPOW + permissions: + id-token: write + if: | + github.repository == 'Becksteinlab/MDPOW' && + (github.event_name == 'release' && github.event.action == 'published') + name: "PyPi: Build and upload pure Python wheels" + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: pypi_deploy + uses: MDAnalysis/pypi-deployment@main + if: github.event_name == 'release' && github.event.action == 'published' + with: + package_name: 'MDPOW' + module_name: 'mdpow' + tests: false diff --git a/.gitignore b/.gitignore index ed42a5df..0a5924b1 100644 --- a/.gitignore +++ b/.gitignore @@ -15,3 +15,11 @@ coverage.xml *.lock *.npz dir.csv + +# Files for the Martini example that can be downloaded at runtime +doc/examples/martini/* +!doc/examples/martini/*.mdp +!doc/examples/martini/*.ipynb +!doc/examples/martini/water.gro +!doc/examples/martini/octanol.gro +!doc/examples/martini/benzene.pdb diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 479fbf75..4ee85489 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,6 +5,11 @@ # Required version: 2 +build: + os: "ubuntu-22.04" + tools: + python: "mambaforge-22.9" + # Build documentation in the docs/ directory with Sphinx sphinx: configuration: doc/sphinx/source/conf.py @@ -13,9 +18,12 @@ sphinx: formats: - pdf -# Optionally set the version of Python and requirements required to build your docs +# install package python: - version: 3.8 install: - - requirements: doc/requirements.txt - system_packages: true \ No newline at end of file + - method: pip + path: . + +conda: + environment: devtools/conda-envs/readthedocs.yaml + diff --git a/.vscode/settings.json b/.vscode/settings.json index ea9d4d09..5124b543 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,5 +1,10 @@ { "[python]": { "editor.formatOnSave": true - } + }, + "python.testing.pytestArgs": [ + "mdpow" + ], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true } \ No newline at end of file diff --git a/AUTHORS b/AUTHORS index 19708124..5194606f 100644 --- a/AUTHORS +++ b/AUTHORS @@ -42,4 +42,4 @@ their first commit. GitHub handle is optional. 2023 ---- -- Alexander Moriarty (@a-ws-m) +- Alexander Moriarty (a-ws-m) diff --git a/CHANGES b/CHANGES index d9cc73f0..5e2bf36b 100644 --- a/CHANGES +++ b/CHANGES @@ -5,15 +5,19 @@ CHANGES for MDPOW Add summary of changes for each release. Use ISO 8061 dates. Reference GitHub issues numbers and PR numbers. -2023-??-?? 0.9.0 +2024-10-11 0.9.0 cadeduckworth, orbeckst, VOD555, a-ws-m Changes -* added support for Python 3.10 (#202) -* dropped testing on Python 3.6 (PR #220, #202) -* dropped testing on Python 3.7 (minimally supported Python >= 3.8, #248) -* support Gromacs 2022.4 and 2023.1 (#256) +* change in TI implementation in fep.Gsolv.analysis(): scipy.integrate.simpson() + now always uses Cartwright's approach to compute the last interval instead of + the old `even="last"` behavior. This change **may lead to small numerical + differences in output** (#281) +* added testing/support for Python 3.10 (#202) to 3.12 (#283) +* dropped testing/support for Python 3.9 (#286), 3.8 (#281), 3.7 (#248), + 3.6 (PR #220, #202) +* support Gromacs 2022.4 and 2023.1 (#256) and 2024.3 (PR #290) * use pymbar >= 4 and alchemlyb >= 2 (#246) * for ensemble.EnsembleAnalysis._single_frame() changed 'pass' to 'raise NotImplementedError' (#216) @@ -25,6 +29,22 @@ Changes EnsembleAnalysis.run() method, no longer needed (per comments, #199) * internal log_banner() now uses logger as argument (PR #247) * use `black` formatter for codebase (#271) +* implemented `forcefields.Forcefield` class (#267) + - facilitates users using non-default forcefields without changing package + code + - `equil.Simulation` has new `ff_class` argument + - each `Forcefield` has unique `default_water_model`, replacing global + `DEFAULT_WATER_MODEL` + - `get_solvent_model()` and `get_solvent_identifier()` take either `str` or + `Forcefield` type for the `forcefield` argument + - both functions also use the `Forcefield`-specific `default_water_model` + (fixes #112) +* `forcefields.DEFAULT_WATER_MODEL` removed (#267) +* changed `system.top` and `system_octwet.top` to act as templates and added + `.template` suffix (#267) +* removed `forcefields.get_ff_paths()` (#267) +* changed `forcefields.get_solvent_identifier()`: will raise `ValueError` + instead of returning `None` (#267) Enhancements @@ -52,6 +72,11 @@ Fixes to explicitly make a copy DataFrame of the data for angle padding (#242) * fix rcoulomb in CHARMM energy minimization MDP template file (PR #210) * fix ensemble.EnsembleAnalysis.check_groups_from_common_ensemble (#212) +* updated versioneer (#285) +* fix that simulation stages cannot be restarted after error (#272) +* fix that testing resource data files were not packaged at all; they are now + included with the sdist (tar.gz) (23 MiB) but excluded from the wheel (whl) + (2.3 MiB) (#293) 2022-01-03 0.8.0 diff --git a/INSTALL.rst b/INSTALL.rst index 093a4740..fd39e996 100644 --- a/INSTALL.rst +++ b/INSTALL.rst @@ -28,7 +28,7 @@ GROMACS_. Conda environment with pre-requisites ------------------------------------- -Make a conda environment with the latest packages for Python 3.8 or +Make a conda environment with the latest packages for Python 3.10 or higher with the name *mdpow*; this installs the larger dependencies that are pre-requisites for MDPOW:: diff --git a/MANIFEST.in b/MANIFEST.in index 683b565b..93a70fe0 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,7 +1,7 @@ -include setup.py setup.cfg COPYING INSTALL README.rst AUTHORS CHANGES -recursive-include doc *.html *.css *.js *.txt *.inv *.png +include setup.py setup.cfg COPYING INSTALL.rst README.rst AUTHORS CHANGES +include versioneer.py +include mdpow/_version.py graft mdpow/templates/ graft mdpow/top/ -graft mdpow/top/oplsaa.ff/ -include versioneer.py -include mdpow/_version.py +graft mdpow/tests/testing_resources/ +global-exclude *.py[cod] \ No newline at end of file diff --git a/README.rst b/README.rst index 7c4e37c1..e95f999d 100644 --- a/README.rst +++ b/README.rst @@ -46,10 +46,10 @@ Installation ------------ See `INSTALL`_ for detailed instructions. MDPOW currently supports and -is tested with Python 3.8 to 3.10. +is tested with Python 3.10 to 3.12. You will also need `Gromacs`_ (currently tested with versions 4.6.5, -2018, 2020, 2021, 2022, 2023 but 2016 and 2019 should also work). +2018, 2020, 2021, 2022, 2023, 2024 but 2016 and 2019 should also work). Development version diff --git a/devtools/conda-envs/readthedocs.yaml b/devtools/conda-envs/readthedocs.yaml new file mode 100644 index 00000000..a9d7747b --- /dev/null +++ b/devtools/conda-envs/readthedocs.yaml @@ -0,0 +1,26 @@ +name: readthedocs +channels: +- conda-forge +dependencies: +- python >=3.10 +- six +- numpy +- scipy >=1.11.0 +- matplotlib-base +- pandas +- scikit-learn +- pyyaml +- mdanalysis >=2 +- numkit +- gromacswrapper +- alchemlyb >=2 +- pymbar >=4 +- rdkit +- seaborn +- svgutils +- cairosvg +- pypdf + +# sphinx and RTD +- sphinx +- sphinx_rtd_theme \ No newline at end of file diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index c283e3e4..4af7a7ad 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -6,7 +6,7 @@ dependencies: - python - six - numpy -- scipy +- scipy >=1.11.0 - matplotlib-base - pandas - scikit-learn @@ -22,7 +22,7 @@ dependencies: - cairosvg - pypdf - # Testing +# Testing - pytest - pytest-pep8 - pytest-cov diff --git a/doc/examples/martini/benzene.pdb b/doc/examples/martini/benzene.pdb new file mode 100644 index 00000000..a6fdaba3 --- /dev/null +++ b/doc/examples/martini/benzene.pdb @@ -0,0 +1,13 @@ +REMARK GENERATED BY TRJCONV +TITLE This is an auto generated system +REMARK THIS IS A SIMULATION BOX +CRYST1 150.000 150.000 180.000 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 R1 BENZ 1 30.920 6.600 24.160 1.00 0.00 +ATOM 2 R2 BENZ 1 28.820 5.000 23.610 1.00 0.00 +ATOM 3 R3 BENZ 1 29.860 6.580 21.680 1.00 0.00 +TER +ENDMDL +CONECT 1 2 +CONECT 2 3 +CONECT 1 3 diff --git a/doc/examples/martini/em.mdp b/doc/examples/martini/em.mdp new file mode 100644 index 00000000..d807c1a2 --- /dev/null +++ b/doc/examples/martini/em.mdp @@ -0,0 +1,17 @@ +include = +integrator = steep +dt = 0.02 +nsteps = 1000 +nstxout = 0 +nstvout = 0 +nstlog = 100 +nstxtcout = 100 +xtc-precision = 1000 +rlist = 1.0 +coulombtype = Reaction-Field +rcoulomb = 1.0 +epsilon_r = 15 +vdw-type = cutoff +vdw-modifier = Potential-shift-verlet +rvdw = 1.0 +constraints = none diff --git a/doc/examples/martini/eq.mdp b/doc/examples/martini/eq.mdp new file mode 100644 index 00000000..0be94d32 --- /dev/null +++ b/doc/examples/martini/eq.mdp @@ -0,0 +1,24 @@ +include = +dt = 0.005 +nsteps = 25000 +nstxout = 0 +nstvout = 0 +nstlog = 1000 +nstxout-compressed = 1000 +cutoff-scheme = Verlet +coulombtype = Reaction-Field +rcoulomb = 1.1 +epsilon_r = 15 +vdw-type = cutoff +vdw-modifier = Potential-shift-verlet +rvdw = 1.1 +tcoupl = v-rescale +tc-grps = System +tau-t = 1.0 +ref-t = 300 +Pcoupl = c-rescale +Pcoupltype = isotropic +tau-p = 3.0 +compressibility = 3e-4 +ref-p = 1.0 +refcoord_scaling = all diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb new file mode 100644 index 00000000..4ac48b9b --- /dev/null +++ b/doc/examples/martini/martini-benzene.ipynb @@ -0,0 +1,10329 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Example: using a different force field\n", + "\n", + "Here we show how to use MDPOW to calculate partition coefficients using an force field that isn't included in the package. To follow along, install `jupyter` in your `mdpow` environment.\n", + "\n", + "To implement a new force field, you will need:\n", + "\n", + "* `ITP` files for the molecule, the solvents, ions and also the general atom type definitions file (usually just named after the force field itself).\n", + "* `MDP` files for the energy minimisation, initial relaxation, NPT ensemble run and free energy calculation.\n", + "* Structure files (`.gro` or `.pdb`) for the solute and non-aqueous solvent. If you are using a type of water that does not come bundled with GROMACS, like in this example, you will also need to create an equilibrated box of pure water.\n", + "\n", + "The first thing we'll do is to download the files we need for Martini 3.0." + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "from typing import Optional\n", + "\n", + "import gromacs\n", + "import requests as req\n", + "\n", + "\n", + "HERE = Path(\".\")\n", + "MARTINI_FF = HERE / \"martini.ff\"\n", + "MARTINI_FF.mkdir(exist_ok=True)\n", + "\n", + "MARTINI_ITP = MARTINI_FF / \"forcefield.itp\"\n", + "MARTINI_IONS = MARTINI_FF / \"martini_v3.0.0_ions_v1.itp\"\n", + "MARTINI_SMALL_MOLS = MARTINI_FF / \"martini_v3.0.0_small_molecules_v1.itp\"\n", + "MARTINI_SOLVENTS = MARTINI_FF / \"martini_v3.0.0_solvents_v1.itp\"\n", + "BENZENE_ITP = MARTINI_SMALL_MOLS\n", + "\n", + "MARTINI_WATER = HERE / \"water.gro\"\n", + "MARTINI_OCTANOL = HERE / \"octanol.gro\"\n", + "MARTINI_BENZENE = HERE / \"benzene.pdb\"\n", + "\n", + "EM_FILE = HERE / \"em.mdp\"\n", + "EQ_FILE = HERE / \"eq.mdp\"\n", + "RUN_FILE = HERE / \"run.mdp\"\n", + "\n", + "\n", + "def download_file(\n", + " url: str, out: Optional[Path] = None, chunk_size: int = 128, overwrite: bool = False\n", + "):\n", + " \"\"\"Utility function to download files.\"\"\"\n", + " if out is None:\n", + " out = HERE / Path(url).name\n", + "\n", + " if out.exists() and not overwrite:\n", + " return\n", + "\n", + " r = req.get(url, stream=True)\n", + " r.raise_for_status()\n", + "\n", + " with out.open(\"wb\") as f:\n", + " for chunk in r.iter_content(chunk_size=chunk_size):\n", + " f.write(chunk)\n", + "\n", + "\n", + "DOWNLOADS = {\n", + " MARTINI_ITP: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0.itp\",\n", + " MARTINI_IONS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_ions_v1.itp\",\n", + " MARTINI_SMALL_MOLS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_small_molecules_v1.itp\",\n", + " MARTINI_SOLVENTS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_solvents_v1.itp\",\n", + "}\n", + "\n", + "for fname, url in DOWNLOADS.items():\n", + " download_file(url, fname)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This should have downloaded several files to your workspace.\n", + "\n", + "We also need to make a `watermodels.dat` file in the `martini.ff` subdirectory.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "56" + ] + }, + "execution_count": 36, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "WATERMODEL_DAT = MARTINI_FF / \"watermodels.dat\"\n", + "\n", + "WATERMODEL_DAT.write_text(\"martini-water\\tMARTINI-WATER\\tMartini default water model.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Next, we set up the files for the Martini 3.0 forcefield." + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [], + "source": [ + "from mdpow.forcefields import Forcefield, GromacsSolventModel\n", + "\n", + "MARTINI = Forcefield(\n", + " \"Martini\",\n", + " solvent_models={\n", + " \"octanol\": GromacsSolventModel(\n", + " identifier=\"octanol\",\n", + " itp=MARTINI_SOLVENTS.absolute(),\n", + " coordinates=str(MARTINI_OCTANOL.absolute()),\n", + " forcefield=\"Martini\",\n", + " ),\n", + " },\n", + " forcefield_dir=MARTINI_FF.absolute(),\n", + " ions_itp=MARTINI_IONS.absolute(),\n", + " default_water_itp=MARTINI_SOLVENTS.absolute(),\n", + " default_water_model=\"martini-water\",\n", + " water_models={\n", + " \"martini-water\": GromacsSolventModel(\n", + " identifier=\"martini-water\",\n", + " itp=MARTINI_SOLVENTS.absolute(),\n", + " coordinates=str(MARTINI_WATER.absolute()),\n", + " forcefield=\"Martini\",\n", + " ),\n", + " },\n", + ")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Aqueous simulation\n", + "\n", + "We now solvate a benzene molecule in a water box. The first step of this is to set up a `WaterSimulation`, then perform some energy minimisation and create the files needed for relaxation." + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/water.gro'...\n", + " :-) GROMACS - gmx editconf, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 3.0\n", + "\n", + "\n", + "Back Off! I just backed up boxed.gro to ./#boxed.gro.1#\n", + "\n", + "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n", + "\n", + " :-) GROMACS - gmx solvate, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx solvate -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -cp boxed.gro -cs /home/awsm/MDPOW/doc/examples/martini/water.gro -o solvated.gro\n", + "\n", + "Reading solute configuration\n", + "Reading solvent configuration\n", + "\n", + "Initialising inter-atomic distances...\n", + "Generating solvent configuration\n", + "Will generate new solvent configuration of 1x1x1 boxes\n", + "Solvent box contains 1731 atoms in 1731 residues\n", + "Removed 98 solvent atoms due to solvent-solvent overlap\n", + "Removed 0 solvent atoms due to solute-solvent overlap\n", + "Sorting configuration\n", + "Found 1 molecule type:\n", + " W ( 1 atoms): 1633 residues\n", + "Generated solvent containing 1633 atoms in 1633 residues\n", + "Writing generated configuration to solvated.gro\n", + "\n", + "Back Off! I just backed up solvated.gro to ./#solvated.gro.1#\n", + "\n", + "Output configuration contains 1636 atoms in 1634 residues\n", + "Volume : 174.316 (nm^3)\n", + "Density : 2860.16 (g/l)\n", + "Number of solvent molecules: 1633 \n", + "\n", + "Processing topology\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#system.top.2#\n", + "\n", + "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n", + "\n", + "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/water.gro\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note that major changes are planned in future for editconf, to improve usability and utility.\n", + "Read 3 atoms\n", + "Volume: 4050 nm^3, corresponds to roughly 1822500 electrons\n", + "No velocities found\n", + " system size : 0.210 0.160 0.248 (nm)\n", + " diameter : 0.270 (nm)\n", + " center : 2.987 0.606 2.315 (nm)\n", + " box vectors : 15.000 15.000 18.000 (nm)\n", + " box angles : 90.00 90.00 90.00 (degrees)\n", + " box volume :4050.00 (nm^3)\n", + " shift : 1.716 4.097 -0.098 (nm)\n", + "new center : 4.703 4.703 2.217 (nm)\n", + "new box vectors : 6.270 6.270 6.270 (nm)\n", + "new box angles : 60.00 60.00 90.00 (degrees)\n", + "new box volume : 174.32 (nm^3)\n", + "\n", + "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", + " based on residue and atom names, since they could not be\n", + " definitively assigned from the information in your input\n", + " files. These guessed numbers might deviate from the mass\n", + " and radius of the atom type. Please check the output\n", + " files if necessary. Note, that this functionality may\n", + " be removed in a future GROMACS version. Please, consider\n", + " using another file format for your input.\n", + "\n", + "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n", + "from the source below. This means the results may be different\n", + "compared to previous GROMACS versions.\n", + "\n", + "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n", + "A. Bondi\n", + "van der Waals Volumes and Radii\n", + "J. Phys. Chem. 68 (1964) pp. 441-451\n", + "-------- -------- --- Thank You --- -------- --------\n", + "\n", + "Adding line for 1633 solvent molecules with resname (W) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation] After solvation: total charge qtot = 0 = 0\n", + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO Building the main index file 'main.ndx'...\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.2#\n", + "\n", + "GROMACS reminds you: \"Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia.\" (Roald Hoffmann)\n", + "\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -n main.ndx -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.3#\n", + "\n", + "GROMACS reminds you: \"Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia.\" (Roald Hoffmann)\n", + "\n", + " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx trjconv -ur compact -center -boxcenter tric -pbc mol -f ionized.gro -s ionized.tpr -o compact.pdb -n main.ndx\n", + "\n", + "Will write pdb: Protein data bank file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Group 0 ( System) has 1636 elements\n", + "Group 1 ( Other) has 1636 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( W) has 1633 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 1633 elements\n", + "Select a group: Group 0 ( System) has 1636 elements\n", + "Group 1 ( Other) has 1636 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( W) has 1633 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 1633 elements\n", + "Select a group: Reading frames from gro file 'This is an auto generated system', 1636 atoms.\n", + "Reading frame 0 time 0.000 \n", + "Precision of ionized.gro is 0.001 (nm)\n", + "\n", + "Back Off! I just backed up compact.pdb to ./#compact.pdb.1#\n", + "Last frame 0 time 0.000 \n", + " -> frame 0 time 0.000 \n", + "Last written: frame 0 time 0.000\n", + "\n", + "\n", + "GROMACS reminds you: \"Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia.\" (Roald Hoffmann)\n", + "\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -f /tmp/tmp_bobqsmz.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -nov\n", + "\n", + "\n", + "NOTE 1 [file /tmp/tmp_bobqsmz.mdp]:\n", + " For a correct single-point energy evaluation with nsteps = 0, use\n", + " continuation = yes to avoid constraining the input coordinates.\n", + "\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#pp_system.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note that major changes are planned in future for trjconv, to improve usability and utility.\n", + "Select group for centering\n", + "Selected 4: '__main__'\n", + "Select group for output\n", + "Selected 0: 'System'\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "(more than 20 non-matching atom names)\n", + "\n", + "WARNING 1 [file system.top, line 28]:\n", + " 999 non-matching atom names\n", + " atom names from\n", + " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top\n", + " will be used\n", + " atom names from\n", + " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro\n", + " will be ignored\n", + "\n", + "\n", + "\n", + "NOTE 2 [file system.top, line 28]:\n", + " For energy conservation with LINCS, lincs_iter should be 2 or larger.\n", + "\n", + "\n", + "Number of degrees of freedom in T-Coupling group rest is 4902.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "NOTE 3 [file /tmp/tmp_bobqsmz.mdp]:\n", + " NVE simulation with an initial temperature of zero: will use a Verlet\n", + " buffer of 10%. Check your energy drift!\n", + "\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"I Caught It In the Face\" (P.J. Harvey)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top', mdp='em.mdp' ...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'em.mdp': ['maxwarn', 'pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em\n", + "Command line:\n", + " gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -maxwarn 1 -pp processed.top\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -411043105\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "(more than 20 non-matching atom names)\n", + "Analysing residue names:\n", + "There are: 1634 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 0 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "(more than 20 non-matching atom names)\n", + "\n", + "WARNING 1 [file system.top, line 28]:\n", + " 999 non-matching atom names\n", + " atom names from\n", + " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top\n", + " will be used\n", + " atom names from\n", + " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro\n", + " will be ignored\n", + "\n", + "\n", + "Number of degrees of freedom in T-Coupling group rest is 4902.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up em.tpr to ./#em.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Input, output, electricity\" (Joni Mitchell)\n", + "\n", + "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/run.py:423: AutoCorrectionWarning: No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + " warnings.warn(wmsg, category=AutoCorrectionWarning)\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em\n", + "Command line:\n", + " gmx mdrun -v -stepout 10 -deffnm em -c em.pdb\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -71328783\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "(more than 20 non-matching atom names)\n", + "Analysing residue names:\n", + "There are: 1634 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 0 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + "Back Off! I just backed up em.log to ./#em.log.1#\n", + "Reading file em.tpr, VERSION 2023.2 (single precision)\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "\n", + "Back Off! I just backed up em.trr to ./#em.trr.1#\n", + "\n", + "Back Off! I just backed up em.edr to ./#em.edr.1#\n", + "\n", + "Steepest Descents:\n", + " Tolerance (Fmax) = 1.00000e+01\n", + " Number of steps = 1000\n", + "Step= 0, Dmax= 1.0e-02 nm, Epot= 9.59019e+06 Fmax= 1.69656e+07, atom= 149\n", + "Step= 1, Dmax= 1.0e-02 nm, Epot= 6.21902e+06 Fmax= 6.01139e+06, atom= 478\n", + "Step= 2, Dmax= 1.2e-02 nm, Epot= 3.58839e+06 Fmax= 2.70774e+06, atom= 17\n", + "Step= 3, Dmax= 1.4e-02 nm, Epot= 2.18086e+06 Fmax= 1.08770e+06, atom= 1305\n", + "Step= 4, Dmax= 1.7e-02 nm, Epot= 1.25600e+06 Fmax= 5.29430e+05, atom= 1493\n", + "Step= 5, Dmax= 2.1e-02 nm, Epot= 7.79933e+05 Fmax= 2.60389e+05, atom= 1513\n", + "Step= 6, Dmax= 2.5e-02 nm, Epot= 4.76315e+05 Fmax= 1.79135e+05, atom= 1493\n", + "Step= 7, Dmax= 3.0e-02 nm, Epot= 3.20697e+05 Fmax= 2.25612e+05, atom= 544\n", + "Step= 8, Dmax= 3.6e-02 nm, Epot= 2.54493e+05 Fmax= 9.11997e+04, atom= 1513\n", + "Step= 9, Dmax= 4.3e-02 nm, Epot= 1.57693e+05 Fmax= 1.98552e+05, atom= 544\n", + "Step= 10, Dmax= 5.2e-02 nm, Epot= 1.29573e+05 Fmax= 6.97811e+04, atom= 1043\n", + "Step= 11, Dmax= 6.2e-02 nm, Epot= 8.43733e+04 Fmax= 2.96448e+05, atom= 200\n", + "Step= 12, Dmax= 7.4e-02 nm, Epot= 7.16053e+04 Fmax= 2.00453e+04, atom= 200\n", + "Step= 13, Dmax= 8.9e-02 nm, Epot= 1.52004e+04 Fmax= 5.75859e+04, atom= 200\n", + "Step= 14, Dmax= 1.1e-01 nm, Epot= 7.52929e+03 Fmax= 2.23154e+04, atom= 200\n", + "Step= 15, Dmax= 1.3e-01 nm, Epot= -2.26025e+03 Fmax= 3.65146e+04, atom= 1107\n", + "Step= 16, Dmax= 1.5e-01 nm, Epot= -7.31692e+03 Fmax= 3.23004e+04, atom= 1107\n", + "Step= 17, Dmax= 1.8e-01 nm, Epot= -8.75253e+03 Fmax= 1.04774e+05, atom= 898\n", + "Step= 18, Dmax= 2.2e-01 nm, Epot= -1.05838e+04 Fmax= 7.90194e+04, atom= 818\n", + "Step= 20, Dmax= 1.3e-01 nm, Epot= -1.44387e+04 Fmax= 1.77139e+04, atom= 1591\n", + "Step= 22, Dmax= 8.0e-02 nm, Epot= -1.69178e+04 Fmax= 2.36072e+04, atom= 1591\n", + "Step= 23, Dmax= 9.6e-02 nm, Epot= -1.85681e+04 Fmax= 1.69728e+04, atom= 1267\n", + "Step= 24, Dmax= 1.2e-01 nm, Epot= -2.05149e+04 Fmax= 1.35050e+04, atom= 1586\n", + "Step= 26, Dmax= 6.9e-02 nm, Epot= -2.22956e+04 Fmax= 7.78836e+03, atom= 1606\n", + "Step= 27, Dmax= 8.3e-02 nm, Epot= -2.46064e+04 Fmax= 8.23711e+03, atom= 1606\n", + "Step= 28, Dmax= 9.9e-02 nm, Epot= -2.60463e+04 Fmax= 2.03933e+04, atom= 1586\n", + "Step= 29, Dmax= 1.2e-01 nm, Epot= -2.71109e+04 Fmax= 8.51193e+03, atom= 1267\n", + "Step= 30, Dmax= 1.4e-01 nm, Epot= -2.77852e+04 Fmax= 5.10258e+04, atom= 1490\n", + "Step= 31, Dmax= 1.7e-01 nm, Epot= -2.89093e+04 Fmax= 8.58690e+03, atom= 1446\n", + "Step= 32, Dmax= 2.1e-01 nm, Epot= -3.02287e+04 Fmax= 2.27404e+04, atom= 1550\n", + "Step= 34, Dmax= 1.2e-01 nm, Epot= -3.08777e+04 Fmax= 1.66820e+04, atom= 1550\n", + "Step= 35, Dmax= 1.5e-01 nm, Epot= -3.15210e+04 Fmax= 7.84227e+03, atom= 468\n", + "Step= 36, Dmax= 1.8e-01 nm, Epot= -3.26742e+04 Fmax= 4.75746e+03, atom= 1596\n", + "Step= 37, Dmax= 2.1e-01 nm, Epot= -3.33775e+04 Fmax= 3.33251e+04, atom= 1461\n", + "Step= 38, Dmax= 2.6e-01 nm, Epot= -3.44663e+04 Fmax= 4.50561e+03, atom= 1596\n", + "Step= 40, Dmax= 1.5e-01 nm, Epot= -3.54502e+04 Fmax= 1.55014e+03, atom= 430\n", + "Step= 41, Dmax= 1.8e-01 nm, Epot= -3.68978e+04 Fmax= 1.01690e+04, atom= 430\n", + "Step= 43, Dmax= 1.1e-01 nm, Epot= -3.73994e+04 Fmax= 2.71559e+03, atom= 1090\n", + "Step= 44, Dmax= 1.3e-01 nm, Epot= -3.78346e+04 Fmax= 2.32965e+03, atom= 1200\n", + "Step= 45, Dmax= 1.6e-01 nm, Epot= -3.80156e+04 Fmax= 6.23591e+03, atom= 1363\n", + "Step= 47, Dmax= 9.6e-02 nm, Epot= -3.85621e+04 Fmax= 2.23179e+03, atom= 867\n", + "Step= 48, Dmax= 1.1e-01 nm, Epot= -3.89186e+04 Fmax= 1.51574e+03, atom= 666\n", + "Step= 50, Dmax= 6.9e-02 nm, Epot= -3.92438e+04 Fmax= 1.20551e+03, atom= 1190\n", + "Step= 52, Dmax= 4.1e-02 nm, Epot= -3.94255e+04 Fmax= 1.81594e+03, atom= 1190\n", + "Step= 53, Dmax= 5.0e-02 nm, Epot= -3.95620e+04 Fmax= 1.81514e+03, atom= 1190\n", + "Step= 54, Dmax= 6.0e-02 nm, Epot= -3.96129e+04 Fmax= 3.54761e+03, atom= 1190\n", + "Step= 55, Dmax= 7.1e-02 nm, Epot= -3.97852e+04 Fmax= 1.91578e+03, atom= 652\n", + "Step= 57, Dmax= 4.3e-02 nm, Epot= -3.99180e+04 Fmax= 1.12184e+03, atom= 1469\n", + "Step= 58, Dmax= 5.1e-02 nm, Epot= -4.00826e+04 Fmax= 1.67238e+03, atom= 652\n", + "Step= 59, Dmax= 6.2e-02 nm, Epot= -4.01535e+04 Fmax= 2.68774e+03, atom= 652\n", + "Step= 60, Dmax= 7.4e-02 nm, Epot= -4.02825e+04 Fmax= 2.17868e+03, atom= 1190\n", + "Step= 61, Dmax= 8.9e-02 nm, Epot= -4.03033e+04 Fmax= 2.91221e+03, atom= 1190\n", + "Step= 63, Dmax= 5.3e-02 nm, Epot= -4.05242e+04 Fmax= 7.05796e+02, atom= 5920\n", + "Step= 64, Dmax= 6.4e-02 nm, Epot= -4.07518e+04 Fmax= 1.27201e+03, atom= 620\n", + "Step= 66, Dmax= 3.8e-02 nm, Epot= -4.08795e+04 Fmax= 1.06263e+03, atom= 620\n", + "Step= 67, Dmax= 4.6e-02 nm, Epot= -4.09734e+04 Fmax= 1.25273e+03, atom= 1190\n", + "Step= 68, Dmax= 5.5e-02 nm, Epot= -4.10696e+04 Fmax= 1.23272e+03, atom= 652\n", + "Step= 69, Dmax= 6.6e-02 nm, Epot= -4.10939e+04 Fmax= 2.04464e+03, atom= 652\n", + "Step= 70, Dmax= 8.0e-02 nm, Epot= -4.11802e+04 Fmax= 2.15417e+03, atom= 652\n", + "Step= 72, Dmax= 4.8e-02 nm, Epot= -4.13412e+04 Fmax= 5.26577e+02, atom= 1469\n", + "Step= 73, Dmax= 5.7e-02 nm, Epot= -4.14448e+04 Fmax= 4.39032e+03, atom= 113\n", + "Step= 74, Dmax= 6.9e-02 nm, Epot= -4.15754e+04 Fmax= 1.06623e+03, atom= 170\n", + "Step= 75, Dmax= 8.3e-02 nm, Epot= -4.16106e+04 Fmax= 4.02645e+03, atom= 170\n", + "Step= 76, Dmax= 9.9e-02 nm, Epot= -4.17108e+04 Fmax= 1.42297e+03, atom= 113\n", + "Step= 78, Dmax= 5.9e-02 nm, Epot= -4.18203e+04 Fmax= 6.25564e+02, atom= 1281\n", + "Step= 79, Dmax= 7.1e-02 nm, Epot= -4.19431e+04 Fmax= 1.31156e+03, atom= 1281\n", + "Step= 81, Dmax= 4.3e-02 nm, Epot= -4.20475e+04 Fmax= 6.75956e+02, atom= 170\n", + "Step= 82, Dmax= 5.1e-02 nm, Epot= -4.21342e+04 Fmax= 8.44703e+02, atom= 170\n", + "Step= 83, Dmax= 6.2e-02 nm, Epot= -4.22080e+04 Fmax= 1.08376e+03, atom= 170\n", + "Step= 84, Dmax= 7.4e-02 nm, Epot= -4.22579e+04 Fmax= 1.35636e+03, atom= 170\n", + "Step= 85, Dmax= 8.9e-02 nm, Epot= -4.23002e+04 Fmax= 1.18031e+03, atom= 1281\n", + "Step= 87, Dmax= 5.3e-02 nm, Epot= -4.24241e+04 Fmax= 5.93261e+02, atom= 240\n", + "Step= 88, Dmax= 6.4e-02 nm, Epot= -4.24516e+04 Fmax= 1.85303e+03, atom= 850\n", + "Step= 89, Dmax= 7.7e-02 nm, Epot= -4.25603e+04 Fmax= 1.13979e+03, atom= 850\n", + "Step= 91, Dmax= 4.6e-02 nm, Epot= -4.26388e+04 Fmax= 4.70422e+02, atom= 70\n", + "Step= 92, Dmax= 5.5e-02 nm, Epot= -4.27223e+04 Fmax= 7.49647e+02, atom= 70\n", + "Step= 94, Dmax= 3.3e-02 nm, Epot= -4.27898e+04 Fmax= 3.79446e+02, atom= 1589\n", + "Step= 95, Dmax= 4.0e-02 nm, Epot= -4.28411e+04 Fmax= 1.38630e+03, atom= 1589\n", + "Step= 96, Dmax= 4.8e-02 nm, Epot= -4.29084e+04 Fmax= 4.60233e+02, atom= 434\n", + "Step= 97, Dmax= 5.7e-02 nm, Epot= -4.29653e+04 Fmax= 1.77860e+03, atom= 434\n", + "Step= 98, Dmax= 6.9e-02 nm, Epot= -4.30177e+04 Fmax= 6.70254e+02, atom= 1589\n", + "Step= 100, Dmax= 4.1e-02 nm, Epot= -4.30756e+04 Fmax= 4.30153e+02, atom= 3179\n", + "Step= 101, Dmax= 4.9e-02 nm, Epot= -4.31321e+04 Fmax= 8.24552e+02, atom= 1589\n", + "Step= 102, Dmax= 5.9e-02 nm, Epot= -4.31471e+04 Fmax= 1.75411e+03, atom= 1589\n", + "Step= 103, Dmax= 7.1e-02 nm, Epot= -4.32164e+04 Fmax= 6.37465e+02, atom= 434\n", + "Step= 104, Dmax= 8.5e-02 nm, Epot= -4.32407e+04 Fmax= 2.03419e+03, atom= 434\n", + "Step= 105, Dmax= 1.0e-01 nm, Epot= -4.32805e+04 Fmax= 1.15510e+03, atom= 1589\n", + "Step= 107, Dmax= 6.2e-02 nm, Epot= -4.33413e+04 Fmax= 7.60702e+02, atom= 317\n", + "Step= 108, Dmax= 7.4e-02 nm, Epot= -4.33930e+04 Fmax= 5.24166e+02, atom= 421\n", + "Step= 110, Dmax= 4.4e-02 nm, Epot= -4.34409e+04 Fmax= 4.94250e+02, atom= 1310\n", + "Step= 111, Dmax= 5.3e-02 nm, Epot= -4.34520e+04 Fmax= 7.46669e+02, atom= 809\n", + "Step= 112, Dmax= 6.4e-02 nm, Epot= -4.34530e+04 Fmax= 1.01330e+03, atom= 1338\n", + "Step= 113, Dmax= 7.7e-02 nm, Epot= -4.34772e+04 Fmax= 9.73190e+02, atom= 1338\n", + "Step= 115, Dmax= 4.6e-02 nm, Epot= -4.36055e+04 Fmax= 2.26279e+02, atom= 8764\n", + "Step= 117, Dmax= 2.8e-02 nm, Epot= -4.36482e+04 Fmax= 3.53046e+02, atom= 9764\n", + "Step= 118, Dmax= 3.3e-02 nm, Epot= -4.36615e+04 Fmax= 5.72281e+02, atom= 97\n", + "Step= 119, Dmax= 4.0e-02 nm, Epot= -4.37004e+04 Fmax= 5.89451e+02, atom= 97\n", + "Step= 120, Dmax= 4.8e-02 nm, Epot= -4.37113e+04 Fmax= 7.40817e+02, atom= 97\n", + "Step= 121, Dmax= 5.7e-02 nm, Epot= -4.37209e+04 Fmax= 8.89442e+02, atom= 97\n", + "Step= 123, Dmax= 3.4e-02 nm, Epot= -4.37990e+04 Fmax= 2.50053e+02, atom= 292\n", + "Step= 124, Dmax= 4.1e-02 nm, Epot= -4.38149e+04 Fmax= 1.67266e+03, atom= 983\n", + "Step= 125, Dmax= 4.9e-02 nm, Epot= -4.38634e+04 Fmax= 4.25221e+02, atom= 983\n", + "Step= 127, Dmax= 3.0e-02 nm, Epot= -4.38911e+04 Fmax= 2.60399e+02, atom= 983\n", + "Step= 128, Dmax= 3.6e-02 nm, Epot= -4.39122e+04 Fmax= 8.88130e+02, atom= 983\n", + "Step= 129, Dmax= 4.3e-02 nm, Epot= -4.39451e+04 Fmax= 4.05544e+02, atom= 983\n", + "Step= 131, Dmax= 2.6e-02 nm, Epot= -4.39673e+04 Fmax= 2.67327e+02, atom= 983\n", + "Step= 132, Dmax= 3.1e-02 nm, Epot= -4.39873e+04 Fmax= 7.50607e+02, atom= 983\n", + "Step= 133, Dmax= 3.7e-02 nm, Epot= -4.40119e+04 Fmax= 3.91773e+02, atom= 983\n", + "Step= 134, Dmax= 4.4e-02 nm, Epot= -4.40212e+04 Fmax= 1.06100e+03, atom= 983\n", + "Step= 135, Dmax= 5.3e-02 nm, Epot= -4.40482e+04 Fmax= 5.30381e+02, atom= 983\n", + "Step= 137, Dmax= 3.2e-02 nm, Epot= -4.40755e+04 Fmax= 2.33595e+02, atom= 1550\n", + "Step= 138, Dmax= 3.8e-02 nm, Epot= -4.40792e+04 Fmax= 1.02432e+03, atom= 983\n", + "Step= 139, Dmax= 4.6e-02 nm, Epot= -4.41246e+04 Fmax= 5.36538e+02, atom= 983\n", + "Step= 140, Dmax= 5.5e-02 nm, Epot= -4.41284e+04 Fmax= 8.92441e+02, atom= 983\n", + "Step= 141, Dmax= 6.6e-02 nm, Epot= -4.41372e+04 Fmax= 9.81172e+02, atom= 983\n", + "Step= 143, Dmax= 4.0e-02 nm, Epot= -4.41830e+04 Fmax= 2.21421e+02, atom= 292\n", + "Step= 144, Dmax= 4.8e-02 nm, Epot= -4.41959e+04 Fmax= 9.82634e+02, atom= 681\n", + "Step= 145, Dmax= 5.7e-02 nm, Epot= -4.42008e+04 Fmax= 1.27957e+03, atom= 983\n", + "Step= 146, Dmax= 6.8e-02 nm, Epot= -4.42377e+04 Fmax= 5.80174e+02, atom= 983\n", + "Step= 148, Dmax= 4.1e-02 nm, Epot= -4.42668e+04 Fmax= 3.80146e+02, atom= 681\n", + "Step= 150, Dmax= 2.5e-02 nm, Epot= -4.42906e+04 Fmax= 1.43903e+02, atom= 681\n", + "Step= 151, Dmax= 3.0e-02 nm, Epot= -4.42986e+04 Fmax= 8.00341e+02, atom= 681\n", + "Step= 152, Dmax= 3.5e-02 nm, Epot= -4.43427e+04 Fmax= 2.10513e+02, atom= 681\n", + "Step= 154, Dmax= 2.1e-02 nm, Epot= -4.43587e+04 Fmax= 3.21124e+02, atom= 681\n", + "Step= 155, Dmax= 2.6e-02 nm, Epot= -4.43728e+04 Fmax= 3.68379e+02, atom= 681\n", + "Step= 156, Dmax= 3.1e-02 nm, Epot= -4.43838e+04 Fmax= 4.31187e+02, atom= 681\n", + "Step= 157, Dmax= 3.7e-02 nm, Epot= -4.43941e+04 Fmax= 5.81376e+02, atom= 681\n", + "Step= 158, Dmax= 4.4e-02 nm, Epot= -4.44034e+04 Fmax= 5.63750e+02, atom= 681\n", + "Step= 160, Dmax= 2.6e-02 nm, Epot= -4.44308e+04 Fmax= 9.28600e+01, atom= 983\n", + "Step= 161, Dmax= 3.2e-02 nm, Epot= -4.44547e+04 Fmax= 8.00824e+02, atom= 983\n", + "Step= 162, Dmax= 3.8e-02 nm, Epot= -4.44837e+04 Fmax= 4.80872e+02, atom= 681\n", + "Step= 164, Dmax= 2.3e-02 nm, Epot= -4.44992e+04 Fmax= 2.08877e+02, atom= 681\n", + "Step= 165, Dmax= 2.7e-02 nm, Epot= -4.45087e+04 Fmax= 5.78343e+02, atom= 681\n", + "Step= 166, Dmax= 3.3e-02 nm, Epot= -4.45223e+04 Fmax= 3.13594e+02, atom= 681\n", + "Step= 168, Dmax= 2.0e-02 nm, Epot= -4.45345e+04 Fmax= 1.32850e+02, atom= 681\n", + "Step= 169, Dmax= 2.4e-02 nm, Epot= -4.45434e+04 Fmax= 5.16686e+02, atom= 681\n", + "Step= 170, Dmax= 2.8e-02 nm, Epot= -4.45622e+04 Fmax= 2.22004e+02, atom= 681\n", + "Step= 172, Dmax= 1.7e-02 nm, Epot= -4.45718e+04 Fmax= 2.13735e+02, atom= 681\n", + "Step= 173, Dmax= 2.1e-02 nm, Epot= -4.45806e+04 Fmax= 3.12405e+02, atom= 681\n", + "Step= 174, Dmax= 2.5e-02 nm, Epot= -4.45886e+04 Fmax= 3.18511e+02, atom= 681\n", + "Step= 175, Dmax= 3.0e-02 nm, Epot= -4.45949e+04 Fmax= 4.49565e+02, atom= 681\n", + "Step= 176, Dmax= 3.5e-02 nm, Epot= -4.46012e+04 Fmax= 4.41628e+02, atom= 681\n", + "Step= 177, Dmax= 4.3e-02 nm, Epot= -4.46024e+04 Fmax= 6.80731e+02, atom= 681\n", + "Step= 178, Dmax= 5.1e-02 nm, Epot= -4.46087e+04 Fmax= 5.79259e+02, atom= 681\n", + "Step= 180, Dmax= 3.1e-02 nm, Epot= -4.46340e+04 Fmax= 1.09441e+02, atom= 983\n", + "Step= 182, Dmax= 1.8e-02 nm, Epot= -4.46458e+04 Fmax= 2.53528e+02, atom= 983\n", + "Step= 183, Dmax= 2.2e-02 nm, Epot= -4.46526e+04 Fmax= 3.37533e+02, atom= 681\n", + "Step= 184, Dmax= 2.6e-02 nm, Epot= -4.46607e+04 Fmax= 3.22827e+02, atom= 681\n", + "Step= 185, Dmax= 3.2e-02 nm, Epot= -4.46640e+04 Fmax= 4.85920e+02, atom= 681\n", + "Step= 186, Dmax= 3.8e-02 nm, Epot= -4.46706e+04 Fmax= 4.41631e+02, atom= 681\n", + "Step= 188, Dmax= 2.3e-02 nm, Epot= -4.46878e+04 Fmax= 6.99539e+01, atom= 983\n", + "Step= 189, Dmax= 2.7e-02 nm, Epot= -4.46916e+04 Fmax= 6.72942e+02, atom= 983\n", + "Step= 190, Dmax= 3.3e-02 nm, Epot= -4.47196e+04 Fmax= 3.42267e+02, atom= 681\n", + "Step= 192, Dmax= 2.0e-02 nm, Epot= -4.47291e+04 Fmax= 1.69135e+02, atom= 681\n", + "Step= 193, Dmax= 2.4e-02 nm, Epot= -4.47341e+04 Fmax= 4.38089e+02, atom= 681\n", + "Step= 194, Dmax= 2.8e-02 nm, Epot= -4.47428e+04 Fmax= 2.60042e+02, atom= 681\n", + "Step= 196, Dmax= 1.7e-02 nm, Epot= -4.47509e+04 Fmax= 1.00247e+02, atom= 681\n", + "Step= 197, Dmax= 2.0e-02 nm, Epot= -4.47564e+04 Fmax= 4.08079e+02, atom= 681\n", + "Step= 198, Dmax= 2.5e-02 nm, Epot= -4.47696e+04 Fmax= 1.69258e+02, atom= 681\n", + "Step= 200, Dmax= 1.5e-02 nm, Epot= -4.47760e+04 Fmax= 1.79183e+02, atom= 681\n", + "Step= 201, Dmax= 1.8e-02 nm, Epot= -4.47820e+04 Fmax= 2.30397e+02, atom= 681\n", + "Step= 202, Dmax= 2.1e-02 nm, Epot= -4.47871e+04 Fmax= 2.66957e+02, atom= 681\n", + "Step= 203, Dmax= 2.5e-02 nm, Epot= -4.47922e+04 Fmax= 3.29333e+02, atom= 681\n", + "Step= 204, Dmax= 3.1e-02 nm, Epot= -4.47953e+04 Fmax= 3.71861e+02, atom= 681\n", + "Step= 205, Dmax= 3.7e-02 nm, Epot= -4.47976e+04 Fmax= 4.93454e+02, atom= 681\n", + "Step= 206, Dmax= 4.4e-02 nm, Epot= -4.47986e+04 Fmax= 4.95148e+02, atom= 681\n", + "Step= 208, Dmax= 2.6e-02 nm, Epot= -4.48210e+04 Fmax= 6.43185e+01, atom= 983\n", + "Step= 210, Dmax= 1.6e-02 nm, Epot= -4.48271e+04 Fmax= 2.21498e+02, atom= 681\n", + "Step= 211, Dmax= 1.9e-02 nm, Epot= -4.48332e+04 Fmax= 2.63512e+02, atom= 642\n", + "Step= 212, Dmax= 2.3e-02 nm, Epot= -4.48369e+04 Fmax= 2.88733e+02, atom= 642\n", + "Step= 213, Dmax= 2.7e-02 nm, Epot= -4.48374e+04 Fmax= 4.27319e+02, atom= 642\n", + "Step= 214, Dmax= 3.3e-02 nm, Epot= -4.48457e+04 Fmax= 3.65651e+02, atom= 642\n", + "Step= 216, Dmax= 2.0e-02 nm, Epot= -4.48645e+04 Fmax= 6.75728e+01, atom= 566\n", + "Step= 218, Dmax= 1.2e-02 nm, Epot= -4.48702e+04 Fmax= 2.10278e+02, atom= 642\n", + "Step= 219, Dmax= 1.4e-02 nm, Epot= -4.48787e+04 Fmax= 1.59517e+02, atom= 642\n", + "Step= 220, Dmax= 1.7e-02 nm, Epot= -4.48816e+04 Fmax= 2.37098e+02, atom= 642\n", + "Step= 221, Dmax= 2.0e-02 nm, Epot= -4.48863e+04 Fmax= 2.64822e+02, atom= 642\n", + "Step= 222, Dmax= 2.5e-02 nm, Epot= -4.48878e+04 Fmax= 3.15225e+02, atom= 642\n", + "Step= 223, Dmax= 2.9e-02 nm, Epot= -4.48880e+04 Fmax= 4.17213e+02, atom= 642\n", + "Step= 224, Dmax= 3.5e-02 nm, Epot= -4.48898e+04 Fmax= 4.16968e+02, atom= 642\n", + "Step= 226, Dmax= 2.1e-02 nm, Epot= -4.49124e+04 Fmax= 8.02827e+01, atom= 1517\n", + "Step= 228, Dmax= 1.3e-02 nm, Epot= -4.49177e+04 Fmax= 2.24192e+02, atom= 809\n", + "Step= 229, Dmax= 1.5e-02 nm, Epot= -4.49250e+04 Fmax= 1.52218e+02, atom= 809\n", + "Step= 230, Dmax= 1.8e-02 nm, Epot= -4.49260e+04 Fmax= 2.90450e+02, atom= 809\n", + "Step= 231, Dmax= 2.2e-02 nm, Epot= -4.49326e+04 Fmax= 2.40121e+02, atom= 809\n", + "Step= 233, Dmax= 1.3e-02 nm, Epot= -4.49417e+04 Fmax= 6.49885e+01, atom= 401\n", + "Step= 235, Dmax= 7.9e-03 nm, Epot= -4.49471e+04 Fmax= 1.35759e+02, atom= 401\n", + "Step= 236, Dmax= 9.5e-03 nm, Epot= -4.49523e+04 Fmax= 1.08182e+02, atom= 401\n", + "Step= 237, Dmax= 1.1e-02 nm, Epot= -4.49565e+04 Fmax= 1.81130e+02, atom= 401\n", + "Step= 238, Dmax= 1.4e-02 nm, Epot= -4.49614e+04 Fmax= 1.69196e+02, atom= 401\n", + "Step= 239, Dmax= 1.6e-02 nm, Epot= -4.49645e+04 Fmax= 2.52875e+02, atom= 401\n", + "Step= 240, Dmax= 2.0e-02 nm, Epot= -4.49692e+04 Fmax= 2.50626e+02, atom= 401\n", + "Step= 241, Dmax= 2.4e-02 nm, Epot= -4.49705e+04 Fmax= 3.65892e+02, atom= 401\n", + "Step= 242, Dmax= 2.8e-02 nm, Epot= -4.49751e+04 Fmax= 3.59765e+02, atom= 401\n", + "Step= 244, Dmax= 1.7e-02 nm, Epot= -4.49854e+04 Fmax= 6.73207e+01, atom= 401\n", + "Step= 246, Dmax= 1.0e-02 nm, Epot= -4.49913e+04 Fmax= 2.18625e+02, atom= 401\n", + "Step= 247, Dmax= 1.2e-02 nm, Epot= -4.49966e+04 Fmax= 1.06170e+02, atom= 401\n", + "Step= 248, Dmax= 1.5e-02 nm, Epot= -4.50010e+04 Fmax= 2.67906e+02, atom= 401\n", + "Step= 249, Dmax= 1.8e-02 nm, Epot= -4.50063e+04 Fmax= 1.80823e+02, atom= 401\n", + "Step= 250, Dmax= 2.1e-02 nm, Epot= -4.50073e+04 Fmax= 3.71151e+02, atom= 401\n", + "Step= 251, Dmax= 2.5e-02 nm, Epot= -4.50133e+04 Fmax= 2.91756e+02, atom= 401\n", + "Step= 253, Dmax= 1.5e-02 nm, Epot= -4.50202e+04 Fmax= 9.03754e+01, atom= 401\n", + "Step= 254, Dmax= 1.8e-02 nm, Epot= -4.50237e+04 Fmax= 4.05349e+02, atom= 401\n", + "Step= 255, Dmax= 2.2e-02 nm, Epot= -4.50323e+04 Fmax= 1.73953e+02, atom= 401\n", + "Step= 257, Dmax= 1.3e-02 nm, Epot= -4.50365e+04 Fmax= 1.37803e+02, atom= 401\n", + "Step= 258, Dmax= 1.6e-02 nm, Epot= -4.50395e+04 Fmax= 2.67295e+02, atom= 401\n", + "Step= 259, Dmax= 1.9e-02 nm, Epot= -4.50443e+04 Fmax= 2.16125e+02, atom= 401\n", + "Step= 260, Dmax= 2.3e-02 nm, Epot= -4.50449e+04 Fmax= 3.64110e+02, atom= 401\n", + "Step= 261, Dmax= 2.7e-02 nm, Epot= -4.50491e+04 Fmax= 3.46302e+02, atom= 401\n", + "Step= 263, Dmax= 1.6e-02 nm, Epot= -4.50579e+04 Fmax= 6.90870e+01, atom= 401\n", + "Step= 264, Dmax= 2.0e-02 nm, Epot= -4.50631e+04 Fmax= 4.63914e+02, atom= 401\n", + "Step= 265, Dmax= 2.4e-02 nm, Epot= -4.50730e+04 Fmax= 1.72436e+02, atom= 401\n", + "Step= 267, Dmax= 1.4e-02 nm, Epot= -4.50768e+04 Fmax= 1.59719e+02, atom= 401\n", + "Step= 268, Dmax= 1.7e-02 nm, Epot= -4.50793e+04 Fmax= 2.67016e+02, atom= 401\n", + "Step= 269, Dmax= 2.0e-02 nm, Epot= -4.50833e+04 Fmax= 2.47747e+02, atom= 401\n", + "Step= 270, Dmax= 2.4e-02 nm, Epot= -4.50836e+04 Fmax= 3.68733e+02, atom= 401\n", + "Step= 271, Dmax= 2.9e-02 nm, Epot= -4.50861e+04 Fmax= 3.95854e+02, atom= 401\n", + "Step= 273, Dmax= 1.8e-02 nm, Epot= -4.50968e+04 Fmax= 5.60686e+01, atom= 401\n", + "Step= 274, Dmax= 2.1e-02 nm, Epot= -4.51039e+04 Fmax= 5.17311e+02, atom= 401\n", + "Step= 275, Dmax= 2.5e-02 nm, Epot= -4.51143e+04 Fmax= 1.85720e+02, atom= 401\n", + "Step= 277, Dmax= 1.5e-02 nm, Epot= -4.51178e+04 Fmax= 1.75657e+02, atom= 401\n", + "Step= 278, Dmax= 1.8e-02 nm, Epot= -4.51196e+04 Fmax= 2.78257e+02, atom= 401\n", + "Step= 279, Dmax= 2.2e-02 nm, Epot= -4.51230e+04 Fmax= 2.73040e+02, atom= 401\n", + "Step= 281, Dmax= 1.3e-02 nm, Epot= -4.51292e+04 Fmax= 5.69754e+01, atom= 401\n", + "Step= 282, Dmax= 1.6e-02 nm, Epot= -4.51354e+04 Fmax= 3.42278e+02, atom= 401\n", + "Step= 283, Dmax= 1.9e-02 nm, Epot= -4.51422e+04 Fmax= 1.44151e+02, atom= 401\n", + "Step= 285, Dmax= 1.1e-02 nm, Epot= -4.51455e+04 Fmax= 1.24741e+02, atom= 401\n", + "Step= 286, Dmax= 1.4e-02 nm, Epot= -4.51481e+04 Fmax= 2.14771e+02, atom= 401\n", + "Step= 287, Dmax= 1.6e-02 nm, Epot= -4.51516e+04 Fmax= 1.94119e+02, atom= 401\n", + "Step= 288, Dmax= 2.0e-02 nm, Epot= -4.51526e+04 Fmax= 2.94393e+02, atom= 401\n", + "Step= 289, Dmax= 2.4e-02 nm, Epot= -4.51553e+04 Fmax= 3.07843e+02, atom= 401\n", + "Step= 291, Dmax= 1.4e-02 nm, Epot= -4.51628e+04 Fmax= 5.11250e+01, atom= 401\n", + "Step= 292, Dmax= 1.7e-02 nm, Epot= -4.51698e+04 Fmax= 3.67684e+02, atom= 401\n", + "Step= 293, Dmax= 2.0e-02 nm, Epot= -4.51767e+04 Fmax= 1.53383e+02, atom= 401\n", + "Step= 295, Dmax= 1.2e-02 nm, Epot= -4.51798e+04 Fmax= 1.39341e+02, atom= 401\n", + "Step= 296, Dmax= 1.5e-02 nm, Epot= -4.51818e+04 Fmax= 2.21630e+02, atom= 401\n", + "Step= 297, Dmax= 1.8e-02 nm, Epot= -4.51849e+04 Fmax= 2.19558e+02, atom= 401\n", + "Step= 298, Dmax= 2.1e-02 nm, Epot= -4.51857e+04 Fmax= 3.01374e+02, atom= 401\n", + "Step= 299, Dmax= 2.5e-02 nm, Epot= -4.51871e+04 Fmax= 3.50012e+02, atom= 401\n", + "Step= 300, Dmax= 3.0e-02 nm, Epot= -4.51874e+04 Fmax= 4.01144e+02, atom= 401\n", + "Step= 302, Dmax= 1.8e-02 nm, Epot= -4.51991e+04 Fmax= 7.91110e+01, atom= 732\n", + "Step= 303, Dmax= 2.2e-02 nm, Epot= -4.51996e+04 Fmax= 4.03636e+02, atom= 732\n", + "Step= 304, Dmax= 2.6e-02 nm, Epot= -4.52062e+04 Fmax= 3.25164e+02, atom= 401\n", + "Step= 306, Dmax= 1.6e-02 nm, Epot= -4.52135e+04 Fmax= 8.16744e+01, atom= 401\n", + "Step= 307, Dmax= 1.9e-02 nm, Epot= -4.52162e+04 Fmax= 3.57140e+02, atom= 401\n", + "Step= 308, Dmax= 2.3e-02 nm, Epot= -4.52222e+04 Fmax= 1.83389e+02, atom= 401\n", + "Step= 310, Dmax= 1.4e-02 nm, Epot= -4.52256e+04 Fmax= 1.33658e+02, atom= 401\n", + "Step= 311, Dmax= 1.6e-02 nm, Epot= -4.52262e+04 Fmax= 2.66531e+02, atom= 401\n", + "Step= 312, Dmax= 2.0e-02 nm, Epot= -4.52303e+04 Fmax= 2.27669e+02, atom= 401\n", + "Step= 314, Dmax= 1.2e-02 nm, Epot= -4.52355e+04 Fmax= 6.32919e+01, atom= 401\n", + "Step= 315, Dmax= 1.4e-02 nm, Epot= -4.52396e+04 Fmax= 2.64077e+02, atom= 401\n", + "Step= 316, Dmax= 1.7e-02 nm, Epot= -4.52444e+04 Fmax= 1.42809e+02, atom= 401\n", + "Step= 318, Dmax= 1.0e-02 nm, Epot= -4.52476e+04 Fmax= 9.54287e+01, atom= 401\n", + "Step= 319, Dmax= 1.2e-02 nm, Epot= -4.52497e+04 Fmax= 2.01162e+02, atom= 401\n", + "Step= 320, Dmax= 1.5e-02 nm, Epot= -4.52533e+04 Fmax= 1.60504e+02, atom= 401\n", + "Step= 321, Dmax= 1.8e-02 nm, Epot= -4.52539e+04 Fmax= 2.62924e+02, atom= 401\n", + "Step= 322, Dmax= 2.1e-02 nm, Epot= -4.52566e+04 Fmax= 2.67672e+02, atom= 401\n", + "Step= 324, Dmax= 1.3e-02 nm, Epot= -4.52632e+04 Fmax= 4.78890e+01, atom= 401\n", + "Step= 325, Dmax= 1.5e-02 nm, Epot= -4.52696e+04 Fmax= 2.89863e+02, atom= 401\n", + "Step= 326, Dmax= 1.8e-02 nm, Epot= -4.52745e+04 Fmax= 1.46259e+02, atom= 1356\n", + "Step= 328, Dmax= 1.1e-02 nm, Epot= -4.52774e+04 Fmax= 1.08762e+02, atom= 401\n", + "Step= 329, Dmax= 1.3e-02 nm, Epot= -4.52790e+04 Fmax= 2.08804e+02, atom= 1356\n", + "Step= 330, Dmax= 1.6e-02 nm, Epot= -4.52823e+04 Fmax= 1.72575e+02, atom= 401\n", + "Step= 332, Dmax= 9.4e-03 nm, Epot= -4.52861e+04 Fmax= 5.70415e+01, atom= 4016\n", + "Step= 333, Dmax= 1.1e-02 nm, Epot= -4.52898e+04 Fmax= 2.05683e+02, atom= 401\n", + "Step= 334, Dmax= 1.4e-02 nm, Epot= -4.52935e+04 Fmax= 1.13823e+02, atom= 401\n", + "Step= 336, Dmax= 8.1e-03 nm, Epot= -4.52962e+04 Fmax= 7.54581e+01, atom= 401\n", + "Step= 337, Dmax= 9.8e-03 nm, Epot= -4.52985e+04 Fmax= 1.61216e+02, atom= 1356\n", + "Step= 338, Dmax= 1.2e-02 nm, Epot= -4.53015e+04 Fmax= 1.20143e+02, atom= 1356\n", + "Step= 339, Dmax= 1.4e-02 nm, Epot= -4.53025e+04 Fmax= 2.19162e+02, atom= 1356\n", + "Step= 340, Dmax= 1.7e-02 nm, Epot= -4.53055e+04 Fmax= 1.87068e+02, atom= 1356\n", + "Step= 342, Dmax= 1.0e-02 nm, Epot= -4.53095e+04 Fmax= 5.70910e+01, atom= 4016\n", + "Step= 343, Dmax= 1.2e-02 nm, Epot= -4.53125e+04 Fmax= 2.22705e+02, atom= 401\n", + "Step= 344, Dmax= 1.5e-02 nm, Epot= -4.53164e+04 Fmax= 1.20191e+02, atom= 1356\n", + "Step= 346, Dmax= 8.8e-03 nm, Epot= -4.53189e+04 Fmax= 8.00550e+01, atom= 1356\n", + "Step= 347, Dmax= 1.1e-02 nm, Epot= -4.53206e+04 Fmax= 1.73454e+02, atom= 1356\n", + "Step= 348, Dmax= 1.3e-02 nm, Epot= -4.53235e+04 Fmax= 1.24943e+02, atom= 1356\n", + "Step= 349, Dmax= 1.5e-02 nm, Epot= -4.53237e+04 Fmax= 2.38134e+02, atom= 1356\n", + "Step= 350, Dmax= 1.8e-02 nm, Epot= -4.53269e+04 Fmax= 1.92623e+02, atom= 1356\n", + "Step= 352, Dmax= 1.1e-02 nm, Epot= -4.53309e+04 Fmax= 6.47061e+01, atom= 4016\n", + "Step= 353, Dmax= 1.3e-02 nm, Epot= -4.53325e+04 Fmax= 2.33340e+02, atom= 401\n", + "Step= 354, Dmax= 1.6e-02 nm, Epot= -4.53366e+04 Fmax= 1.32755e+02, atom= 1356\n", + "Step= 356, Dmax= 9.4e-03 nm, Epot= -4.53391e+04 Fmax= 7.97862e+01, atom= 732\n", + "Step= 357, Dmax= 1.1e-02 nm, Epot= -4.53402e+04 Fmax= 1.90449e+02, atom= 1356\n", + "Step= 358, Dmax= 1.4e-02 nm, Epot= -4.53434e+04 Fmax= 1.26101e+02, atom= 1356\n", + "Step= 360, Dmax= 8.1e-03 nm, Epot= -4.53459e+04 Fmax= 5.88508e+01, atom= 4016\n", + "Step= 361, Dmax= 9.8e-03 nm, Epot= -4.53478e+04 Fmax= 1.65977e+02, atom= 401\n", + "Step= 362, Dmax= 1.2e-02 nm, Epot= -4.53508e+04 Fmax= 1.05645e+02, atom= 1356\n", + "Step= 363, Dmax= 1.4e-02 nm, Epot= -4.53508e+04 Fmax= 2.19347e+02, atom= 1356\n", + "Step= 364, Dmax= 1.7e-02 nm, Epot= -4.53540e+04 Fmax= 1.71196e+02, atom= 1356\n", + "Step= 366, Dmax= 1.0e-02 nm, Epot= -4.53574e+04 Fmax= 6.38905e+01, atom= 7326\n", + "Step= 367, Dmax= 1.2e-02 nm, Epot= -4.53585e+04 Fmax= 2.11677e+02, atom= 732\n", + "Step= 368, Dmax= 1.5e-02 nm, Epot= -4.53621e+04 Fmax= 1.23472e+02, atom= 1356\n", + "Step= 370, Dmax= 8.7e-03 nm, Epot= -4.53644e+04 Fmax= 6.90884e+01, atom= 1356\n", + "Step= 371, Dmax= 1.0e-02 nm, Epot= -4.53655e+04 Fmax= 1.70116e+02, atom= 1356\n", + "Step= 372, Dmax= 1.3e-02 nm, Epot= -4.53684e+04 Fmax= 1.17780e+02, atom= 1356\n", + "Step= 374, Dmax= 7.6e-03 nm, Epot= -4.53708e+04 Fmax= 5.43108e+01, atom= 7326\n", + "Step= 375, Dmax= 9.1e-03 nm, Epot= -4.53727e+04 Fmax= 1.49716e+02, atom= 732\n", + "Step= 376, Dmax= 1.1e-02 nm, Epot= -4.53752e+04 Fmax= 9.37573e+01, atom= 732\n", + "Step= 377, Dmax= 1.3e-02 nm, Epot= -4.53753e+04 Fmax= 2.13574e+02, atom= 732\n", + "Step= 378, Dmax= 1.6e-02 nm, Epot= -4.53787e+04 Fmax= 1.38101e+02, atom= 732\n", + "Step= 380, Dmax= 9.4e-03 nm, Epot= -4.53813e+04 Fmax= 6.41603e+01, atom= 1356\n", + "Step= 381, Dmax= 1.1e-02 nm, Epot= -4.53816e+04 Fmax= 1.92141e+02, atom= 1356\n", + "Step= 382, Dmax= 1.4e-02 nm, Epot= -4.53854e+04 Fmax= 1.15458e+02, atom= 732\n", + "Step= 384, Dmax= 8.1e-03 nm, Epot= -4.53877e+04 Fmax= 6.75705e+01, atom= 7326\n", + "Step= 385, Dmax= 9.7e-03 nm, Epot= -4.53890e+04 Fmax= 1.47951e+02, atom= 732\n", + "Step= 386, Dmax= 1.2e-02 nm, Epot= -4.53914e+04 Fmax= 1.09483e+02, atom= 732\n", + "Step= 388, Dmax= 7.0e-03 nm, Epot= -4.53936e+04 Fmax= 4.14989e+01, atom= 732\n", + "Step= 389, Dmax= 8.4e-03 nm, Epot= -4.53953e+04 Fmax= 1.47392e+02, atom= 732\n", + "Step= 390, Dmax= 1.0e-02 nm, Epot= -4.53985e+04 Fmax= 7.96769e+01, atom= 732\n", + "Step= 392, Dmax= 6.1e-03 nm, Epot= -4.54004e+04 Fmax= 5.41914e+01, atom= 732\n", + "Step= 393, Dmax= 7.3e-03 nm, Epot= -4.54020e+04 Fmax= 1.05904e+02, atom= 732\n", + "Step= 394, Dmax= 8.7e-03 nm, Epot= -4.54040e+04 Fmax= 8.51007e+01, atom= 732\n", + "Step= 395, Dmax= 1.0e-02 nm, Epot= -4.54046e+04 Fmax= 1.49032e+02, atom= 732\n", + "Step= 396, Dmax= 1.3e-02 nm, Epot= -4.54068e+04 Fmax= 1.31882e+02, atom= 1264\n", + "Step= 398, Dmax= 7.5e-03 nm, Epot= -4.54100e+04 Fmax= 3.98925e+01, atom= 7184\n", + "Step= 399, Dmax= 9.0e-03 nm, Epot= -4.54121e+04 Fmax= 1.50702e+02, atom= 718\n", + "Step= 400, Dmax= 1.1e-02 nm, Epot= -4.54150e+04 Fmax= 9.65127e+01, atom= 1264\n", + "Step= 402, Dmax= 6.5e-03 nm, Epot= -4.54170e+04 Fmax= 4.84820e+01, atom= 1264\n", + "Step= 403, Dmax= 7.8e-03 nm, Epot= -4.54188e+04 Fmax= 1.34380e+02, atom= 1264\n", + "Step= 404, Dmax= 9.4e-03 nm, Epot= -4.54212e+04 Fmax= 7.88978e+01, atom= 1264\n", + "Step= 405, Dmax= 1.1e-02 nm, Epot= -4.54219e+04 Fmax= 1.84098e+02, atom= 1264\n", + "Step= 406, Dmax= 1.4e-02 nm, Epot= -4.54247e+04 Fmax= 1.21435e+02, atom= 1264\n", + "Step= 408, Dmax= 8.1e-03 nm, Epot= -4.54270e+04 Fmax= 5.42474e+01, atom= 1264\n", + "Step= 409, Dmax= 9.7e-03 nm, Epot= -4.54283e+04 Fmax= 1.67290e+02, atom= 1264\n", + "Step= 410, Dmax= 1.2e-02 nm, Epot= -4.54313e+04 Fmax= 9.76441e+01, atom= 1264\n", + "Step= 412, Dmax= 7.0e-03 nm, Epot= -4.54332e+04 Fmax= 5.88133e+01, atom= 1264\n", + "Step= 413, Dmax= 8.4e-03 nm, Epot= -4.54349e+04 Fmax= 1.36199e+02, atom= 1264\n", + "Step= 414, Dmax= 1.0e-02 nm, Epot= -4.54371e+04 Fmax= 9.17353e+01, atom= 1264\n", + "Step= 415, Dmax= 1.2e-02 nm, Epot= -4.54378e+04 Fmax= 1.90666e+02, atom= 1264\n", + "Step= 416, Dmax= 1.5e-02 nm, Epot= -4.54403e+04 Fmax= 1.37506e+02, atom= 1264\n", + "Step= 418, Dmax= 8.7e-03 nm, Epot= -4.54429e+04 Fmax= 5.01721e+01, atom= 1264\n", + "Step= 419, Dmax= 1.0e-02 nm, Epot= -4.54440e+04 Fmax= 1.92386e+02, atom= 1264\n", + "Step= 420, Dmax= 1.3e-02 nm, Epot= -4.54478e+04 Fmax= 9.50806e+01, atom= 1264\n", + "Step= 422, Dmax= 7.5e-03 nm, Epot= -4.54497e+04 Fmax= 7.13852e+01, atom= 1264\n", + "Step= 423, Dmax= 9.0e-03 nm, Epot= -4.54511e+04 Fmax= 1.38056e+02, atom= 1264\n", + "Step= 424, Dmax= 1.1e-02 nm, Epot= -4.54533e+04 Fmax= 1.06649e+02, atom= 1264\n", + "Step= 425, Dmax= 1.3e-02 nm, Epot= -4.54538e+04 Fmax= 1.96301e+02, atom= 1264\n", + "Step= 426, Dmax= 1.6e-02 nm, Epot= -4.54563e+04 Fmax= 1.57068e+02, atom= 1264\n", + "Step= 428, Dmax= 9.4e-03 nm, Epot= -4.54594e+04 Fmax= 4.62974e+01, atom= 7184\n", + "Step= 429, Dmax= 1.1e-02 nm, Epot= -4.54602e+04 Fmax= 2.15458e+02, atom= 1264\n", + "Step= 430, Dmax= 1.3e-02 nm, Epot= -4.54652e+04 Fmax= 9.90192e+01, atom= 1264\n", + "Step= 432, Dmax= 8.1e-03 nm, Epot= -4.54671e+04 Fmax= 7.86969e+01, atom= 1264\n", + "Step= 433, Dmax= 9.7e-03 nm, Epot= -4.54684e+04 Fmax= 1.47572e+02, atom= 1264\n", + "Step= 434, Dmax= 1.2e-02 nm, Epot= -4.54709e+04 Fmax= 1.16005e+02, atom= 1264\n", + "Step= 435, Dmax= 1.4e-02 nm, Epot= -4.54709e+04 Fmax= 2.11263e+02, atom= 1264\n", + "Step= 436, Dmax= 1.7e-02 nm, Epot= -4.54738e+04 Fmax= 1.70085e+02, atom= 1264\n", + "Step= 438, Dmax= 1.0e-02 nm, Epot= -4.54776e+04 Fmax= 5.06155e+01, atom= 7184\n", + "Step= 439, Dmax= 1.2e-02 nm, Epot= -4.54778e+04 Fmax= 2.24940e+02, atom= 1264\n", + "Step= 440, Dmax= 1.4e-02 nm, Epot= -4.54834e+04 Fmax= 1.15936e+02, atom= 1264\n", + "Step= 442, Dmax= 8.7e-03 nm, Epot= -4.54858e+04 Fmax= 7.58463e+01, atom= 1264\n", + "Step= 443, Dmax= 1.0e-02 nm, Epot= -4.54868e+04 Fmax= 1.71706e+02, atom= 1264\n", + "Step= 444, Dmax= 1.3e-02 nm, Epot= -4.54899e+04 Fmax= 1.14794e+02, atom= 1264\n", + "Step= 446, Dmax= 7.5e-03 nm, Epot= -4.54925e+04 Fmax= 5.08589e+01, atom= 1264\n", + "Step= 447, Dmax= 9.0e-03 nm, Epot= -4.54943e+04 Fmax= 1.55627e+02, atom= 1264\n", + "Step= 448, Dmax= 1.1e-02 nm, Epot= -4.54977e+04 Fmax= 9.23687e+01, atom= 1264\n", + "Step= 449, Dmax= 1.3e-02 nm, Epot= -4.54977e+04 Fmax= 2.01794e+02, atom= 1264\n", + "Step= 450, Dmax= 1.6e-02 nm, Epot= -4.55013e+04 Fmax= 1.54131e+02, atom= 1264\n", + "Step= 452, Dmax= 9.4e-03 nm, Epot= -4.55048e+04 Fmax= 6.08370e+01, atom= 5824\n", + "Step= 453, Dmax= 1.1e-02 nm, Epot= -4.55061e+04 Fmax= 2.05291e+02, atom= 1264\n", + "Step= 454, Dmax= 1.3e-02 nm, Epot= -4.55102e+04 Fmax= 1.10097e+02, atom= 1264\n", + "Step= 456, Dmax= 8.1e-03 nm, Epot= -4.55126e+04 Fmax= 6.75424e+01, atom= 1264\n", + "Step= 457, Dmax= 9.7e-03 nm, Epot= -4.55144e+04 Fmax= 1.53591e+02, atom= 1264\n", + "Step= 458, Dmax= 1.2e-02 nm, Epot= -4.55173e+04 Fmax= 1.13209e+02, atom= 1264\n", + "Step= 459, Dmax= 1.4e-02 nm, Epot= -4.55178e+04 Fmax= 2.05422e+02, atom= 1264\n", + "Step= 460, Dmax= 1.7e-02 nm, Epot= -4.55208e+04 Fmax= 1.79725e+02, atom= 1264\n", + "Step= 462, Dmax= 1.0e-02 nm, Epot= -4.55248e+04 Fmax= 5.70532e+01, atom= 5824\n", + "Step= 463, Dmax= 1.2e-02 nm, Epot= -4.55270e+04 Fmax= 2.20245e+02, atom= 1264\n", + "Step= 464, Dmax= 1.4e-02 nm, Epot= -4.55310e+04 Fmax= 1.21818e+02, atom= 1264\n", + "Step= 466, Dmax= 8.7e-03 nm, Epot= -4.55335e+04 Fmax= 6.85399e+01, atom= 1264\n", + "Step= 467, Dmax= 1.0e-02 nm, Epot= -4.55354e+04 Fmax= 1.71478e+02, atom= 1264\n", + "Step= 468, Dmax= 1.3e-02 nm, Epot= -4.55386e+04 Fmax= 1.16256e+02, atom= 1264\n", + "Step= 469, Dmax= 1.5e-02 nm, Epot= -4.55389e+04 Fmax= 2.28416e+02, atom= 1264\n", + "Step= 470, Dmax= 1.8e-02 nm, Epot= -4.55423e+04 Fmax= 1.86440e+02, atom= 1264\n", + "Step= 472, Dmax= 1.1e-02 nm, Epot= -4.55462e+04 Fmax= 6.65599e+01, atom= 5824\n", + "Step= 473, Dmax= 1.3e-02 nm, Epot= -4.55479e+04 Fmax= 2.35647e+02, atom= 1264\n", + "Step= 474, Dmax= 1.6e-02 nm, Epot= -4.55520e+04 Fmax= 1.32947e+02, atom= 1264\n", + "Step= 476, Dmax= 9.3e-03 nm, Epot= -4.55546e+04 Fmax= 7.12243e+01, atom= 1264\n", + "Step= 477, Dmax= 1.1e-02 nm, Epot= -4.55563e+04 Fmax= 1.88520e+02, atom= 1264\n", + "Step= 478, Dmax= 1.3e-02 nm, Epot= -4.55597e+04 Fmax= 1.21857e+02, atom= 1264\n", + "Step= 480, Dmax= 8.1e-03 nm, Epot= -4.55622e+04 Fmax= 6.11391e+01, atom= 1264\n", + "Step= 481, Dmax= 9.7e-03 nm, Epot= -4.55645e+04 Fmax= 1.72616e+02, atom= 1264\n", + "Step= 482, Dmax= 1.2e-02 nm, Epot= -4.55675e+04 Fmax= 9.73076e+01, atom= 1264\n", + "Step= 483, Dmax= 1.4e-02 nm, Epot= -4.55682e+04 Fmax= 2.39947e+02, atom= 1264\n", + "Step= 484, Dmax= 1.7e-02 nm, Epot= -4.55718e+04 Fmax= 1.48898e+02, atom= 1264\n", + "Step= 486, Dmax= 1.0e-02 nm, Epot= -4.55746e+04 Fmax= 7.07733e+01, atom= 1264\n", + "Step= 487, Dmax= 1.2e-02 nm, Epot= -4.55758e+04 Fmax= 2.11975e+02, atom= 1264\n", + "Step= 488, Dmax= 1.4e-02 nm, Epot= -4.55797e+04 Fmax= 1.24149e+02, atom= 1264\n", + "Step= 490, Dmax= 8.7e-03 nm, Epot= -4.55820e+04 Fmax= 7.05765e+01, atom= 1264\n", + "Step= 491, Dmax= 1.0e-02 nm, Epot= -4.55838e+04 Fmax= 1.80952e+02, atom= 1264\n", + "Step= 492, Dmax= 1.2e-02 nm, Epot= -4.55867e+04 Fmax= 1.08217e+02, atom= 1264\n", + "Step= 493, Dmax= 1.5e-02 nm, Epot= -4.55869e+04 Fmax= 2.55069e+02, atom= 1264\n", + "Step= 494, Dmax= 1.8e-02 nm, Epot= -4.55905e+04 Fmax= 1.62458e+02, atom= 1264\n", + "Step= 496, Dmax= 1.1e-02 nm, Epot= -4.55934e+04 Fmax= 7.19876e+01, atom= 1264\n", + "Step= 497, Dmax= 1.3e-02 nm, Epot= -4.55939e+04 Fmax= 2.33657e+02, atom= 1264\n", + "Step= 498, Dmax= 1.6e-02 nm, Epot= -4.55982e+04 Fmax= 1.29079e+02, atom= 1264\n", + "Step= 500, Dmax= 9.3e-03 nm, Epot= -4.56005e+04 Fmax= 7.82755e+01, atom= 1264\n", + "Step= 501, Dmax= 1.1e-02 nm, Epot= -4.56017e+04 Fmax= 1.91028e+02, atom= 1264\n", + "Step= 502, Dmax= 1.3e-02 nm, Epot= -4.56045e+04 Fmax= 1.17858e+02, atom= 1264\n", + "Step= 504, Dmax= 8.1e-03 nm, Epot= -4.56067e+04 Fmax= 6.12183e+01, atom= 1264\n", + "Step= 505, Dmax= 9.7e-03 nm, Epot= -4.56084e+04 Fmax= 1.57054e+02, atom= 1264\n", + "Step= 506, Dmax= 1.2e-02 nm, Epot= -4.56109e+04 Fmax= 1.11038e+02, atom= 1264\n", + "Step= 507, Dmax= 1.4e-02 nm, Epot= -4.56113e+04 Fmax= 2.02945e+02, atom= 1264\n", + "Step= 508, Dmax= 1.7e-02 nm, Epot= -4.56137e+04 Fmax= 1.82632e+02, atom= 1264\n", + "Step= 510, Dmax= 1.0e-02 nm, Epot= -4.56170e+04 Fmax= 5.44213e+01, atom= 5824\n", + "Step= 511, Dmax= 1.2e-02 nm, Epot= -4.56188e+04 Fmax= 2.14129e+02, atom= 1264\n", + "Step= 512, Dmax= 1.4e-02 nm, Epot= -4.56219e+04 Fmax= 1.22899e+02, atom= 1264\n", + "Step= 514, Dmax= 8.7e-03 nm, Epot= -4.56240e+04 Fmax= 6.72173e+01, atom= 1264\n", + "Step= 515, Dmax= 1.0e-02 nm, Epot= -4.56252e+04 Fmax= 1.68104e+02, atom= 1264\n", + "Step= 516, Dmax= 1.2e-02 nm, Epot= -4.56278e+04 Fmax= 1.19144e+02, atom= 1264\n", + "Step= 518, Dmax= 7.5e-03 nm, Epot= -4.56298e+04 Fmax= 5.14206e+01, atom= 5824\n", + "Step= 519, Dmax= 9.0e-03 nm, Epot= -4.56316e+04 Fmax= 1.59831e+02, atom= 1264\n", + "Step= 520, Dmax= 1.1e-02 nm, Epot= -4.56341e+04 Fmax= 8.75089e+01, atom= 1264\n", + "Step= 521, Dmax= 1.3e-02 nm, Epot= -4.56341e+04 Fmax= 2.25079e+02, atom= 1264\n", + "Step= 522, Dmax= 1.6e-02 nm, Epot= -4.56374e+04 Fmax= 1.31770e+02, atom= 1264\n", + "Step= 524, Dmax= 9.3e-03 nm, Epot= -4.56396e+04 Fmax= 7.20213e+01, atom= 1264\n", + "Step= 525, Dmax= 1.1e-02 nm, Epot= -4.56401e+04 Fmax= 1.81395e+02, atom= 1264\n", + "Step= 526, Dmax= 1.3e-02 nm, Epot= -4.56429e+04 Fmax= 1.27643e+02, atom= 1264\n", + "Step= 528, Dmax= 8.0e-03 nm, Epot= -4.56452e+04 Fmax= 5.65556e+01, atom= 5824\n", + "Step= 529, Dmax= 9.6e-03 nm, Epot= -4.56462e+04 Fmax= 1.68386e+02, atom= 1264\n", + "Step= 530, Dmax= 1.2e-02 nm, Epot= -4.56490e+04 Fmax= 9.67118e+01, atom= 1264\n", + "Step= 532, Dmax= 6.9e-03 nm, Epot= -4.56508e+04 Fmax= 5.82563e+01, atom= 1264\n", + "Step= 533, Dmax= 8.3e-03 nm, Epot= -4.56519e+04 Fmax= 1.26980e+02, atom= 1264\n", + "Step= 534, Dmax= 1.0e-02 nm, Epot= -4.56539e+04 Fmax= 1.03427e+02, atom= 1264\n", + "Step= 536, Dmax= 6.0e-03 nm, Epot= -4.56560e+04 Fmax= 3.59879e+01, atom= 582\n", + "Step= 537, Dmax= 7.2e-03 nm, Epot= -4.56578e+04 Fmax= 1.31417e+02, atom= 626\n", + "Step= 538, Dmax= 8.6e-03 nm, Epot= -4.56602e+04 Fmax= 7.34455e+01, atom= 626\n", + "Step= 539, Dmax= 1.0e-02 nm, Epot= -4.56603e+04 Fmax= 1.73195e+02, atom= 626\n", + "Step= 540, Dmax= 1.2e-02 nm, Epot= -4.56631e+04 Fmax= 1.21107e+02, atom= 626\n", + "Step= 542, Dmax= 7.5e-03 nm, Epot= -4.56653e+04 Fmax= 5.14276e+01, atom= 626\n", + "Step= 543, Dmax= 9.0e-03 nm, Epot= -4.56662e+04 Fmax= 1.71196e+02, atom= 626\n", + "Step= 544, Dmax= 1.1e-02 nm, Epot= -4.56691e+04 Fmax= 8.82880e+01, atom= 626\n", + "Step= 546, Dmax= 6.5e-03 nm, Epot= -4.56706e+04 Fmax= 6.41895e+01, atom= 626\n", + "Step= 547, Dmax= 7.7e-03 nm, Epot= -4.56720e+04 Fmax= 1.17044e+02, atom= 626\n", + "Step= 548, Dmax= 9.3e-03 nm, Epot= -4.56736e+04 Fmax= 1.02734e+02, atom= 626\n", + "Step= 549, Dmax= 1.1e-02 nm, Epot= -4.56743e+04 Fmax= 1.61741e+02, atom= 626\n", + "Step= 550, Dmax= 1.3e-02 nm, Epot= -4.56759e+04 Fmax= 1.54384e+02, atom= 626\n", + "Step= 552, Dmax= 8.0e-03 nm, Epot= -4.56782e+04 Fmax= 3.38864e+01, atom= 111\n", + "Step= 553, Dmax= 9.6e-03 nm, Epot= -4.56801e+04 Fmax= 2.14097e+02, atom= 626\n", + "Step= 554, Dmax= 1.2e-02 nm, Epot= -4.56835e+04 Fmax= 7.52265e+01, atom= 626\n", + "Step= 556, Dmax= 6.9e-03 nm, Epot= -4.56849e+04 Fmax= 8.64305e+01, atom= 626\n", + "Step= 557, Dmax= 8.3e-03 nm, Epot= -4.56861e+04 Fmax= 1.08619e+02, atom= 626\n", + "Step= 558, Dmax= 1.0e-02 nm, Epot= -4.56873e+04 Fmax= 1.27482e+02, atom= 626\n", + "Step= 559, Dmax= 1.2e-02 nm, Epot= -4.56883e+04 Fmax= 1.56156e+02, atom= 626\n", + "Step= 560, Dmax= 1.4e-02 nm, Epot= -4.56892e+04 Fmax= 1.83907e+02, atom= 626\n", + "Step= 561, Dmax= 1.7e-02 nm, Epot= -4.56895e+04 Fmax= 2.29917e+02, atom= 626\n", + "Step= 562, Dmax= 2.1e-02 nm, Epot= -4.56900e+04 Fmax= 2.59564e+02, atom= 626\n", + "Step= 564, Dmax= 1.2e-02 nm, Epot= -4.56946e+04 Fmax= 4.79706e+01, atom= 111\n", + "Step= 565, Dmax= 1.5e-02 nm, Epot= -4.56952e+04 Fmax= 2.71962e+02, atom= 626\n", + "Step= 566, Dmax= 1.8e-02 nm, Epot= -4.56986e+04 Fmax= 1.97401e+02, atom= 626\n", + "Step= 568, Dmax= 1.1e-02 nm, Epot= -4.57012e+04 Fmax= 5.53465e+01, atom= 339\n", + "Step= 569, Dmax= 1.3e-02 nm, Epot= -4.57014e+04 Fmax= 2.54759e+02, atom= 339\n", + "Step= 570, Dmax= 1.5e-02 nm, Epot= -4.57050e+04 Fmax= 1.19686e+02, atom= 626\n", + "Step= 572, Dmax= 9.3e-03 nm, Epot= -4.57064e+04 Fmax= 8.76655e+01, atom= 626\n", + "Step= 573, Dmax= 1.1e-02 nm, Epot= -4.57068e+04 Fmax= 1.81661e+02, atom= 626\n", + "Step= 574, Dmax= 1.3e-02 nm, Epot= -4.57087e+04 Fmax= 1.36746e+02, atom= 626\n", + "Step= 576, Dmax= 8.0e-03 nm, Epot= -4.57106e+04 Fmax= 5.28007e+01, atom= 626\n", + "Step= 577, Dmax= 9.6e-03 nm, Epot= -4.57117e+04 Fmax= 1.71984e+02, atom= 626\n", + "Step= 578, Dmax= 1.2e-02 nm, Epot= -4.57137e+04 Fmax= 1.01928e+02, atom= 626\n", + "Step= 580, Dmax= 6.9e-03 nm, Epot= -4.57151e+04 Fmax= 5.67850e+01, atom= 626\n", + "Step= 581, Dmax= 8.3e-03 nm, Epot= -4.57161e+04 Fmax= 1.45923e+02, atom= 626\n", + "Step= 582, Dmax= 1.0e-02 nm, Epot= -4.57178e+04 Fmax= 9.20070e+01, atom= 626\n", + "Step= 583, Dmax= 1.2e-02 nm, Epot= -4.57179e+04 Fmax= 1.95271e+02, atom= 626\n", + "Step= 584, Dmax= 1.4e-02 nm, Epot= -4.57198e+04 Fmax= 1.49080e+02, atom= 626\n", + "Step= 586, Dmax= 8.6e-03 nm, Epot= -4.57218e+04 Fmax= 5.45235e+01, atom= 626\n", + "Step= 587, Dmax= 1.0e-02 nm, Epot= -4.57226e+04 Fmax= 1.90014e+02, atom= 626\n", + "Step= 588, Dmax= 1.2e-02 nm, Epot= -4.57249e+04 Fmax= 1.05233e+02, atom= 626\n", + "Step= 590, Dmax= 7.4e-03 nm, Epot= -4.57262e+04 Fmax= 6.50171e+01, atom= 626\n", + "Step= 591, Dmax= 8.9e-03 nm, Epot= -4.57269e+04 Fmax= 1.51520e+02, atom= 626\n", + "Step= 592, Dmax= 1.1e-02 nm, Epot= -4.57286e+04 Fmax= 1.04259e+02, atom= 626\n", + "Step= 594, Dmax= 6.4e-03 nm, Epot= -4.57300e+04 Fmax= 4.86618e+01, atom= 626\n", + "Step= 595, Dmax= 7.7e-03 nm, Epot= -4.57312e+04 Fmax= 1.31234e+02, atom= 626\n", + "Step= 596, Dmax= 9.3e-03 nm, Epot= -4.57327e+04 Fmax= 8.79141e+01, atom= 626\n", + "Step= 597, Dmax= 1.1e-02 nm, Epot= -4.57330e+04 Fmax= 1.77630e+02, atom= 626\n", + "Step= 598, Dmax= 1.3e-02 nm, Epot= -4.57346e+04 Fmax= 1.37288e+02, atom= 626\n", + "Step= 600, Dmax= 8.0e-03 nm, Epot= -4.57364e+04 Fmax= 4.65334e+01, atom= 626\n", + "Step= 601, Dmax= 9.6e-03 nm, Epot= -4.57367e+04 Fmax= 1.97158e+02, atom= 626\n", + "Step= 602, Dmax= 1.2e-02 nm, Epot= -4.57395e+04 Fmax= 8.53432e+01, atom= 626\n", + "Step= 604, Dmax= 6.9e-03 nm, Epot= -4.57406e+04 Fmax= 7.80857e+01, atom= 626\n", + "Step= 605, Dmax= 8.3e-03 nm, Epot= -4.57414e+04 Fmax= 1.17089e+02, atom= 626\n", + "Step= 606, Dmax= 1.0e-02 nm, Epot= -4.57425e+04 Fmax= 1.18012e+02, atom= 626\n", + "Step= 607, Dmax= 1.2e-02 nm, Epot= -4.57429e+04 Fmax= 1.66990e+02, atom= 626\n", + "Step= 608, Dmax= 1.4e-02 nm, Epot= -4.57438e+04 Fmax= 1.71056e+02, atom= 626\n", + "Step= 610, Dmax= 8.6e-03 nm, Epot= -4.57461e+04 Fmax= 3.25288e+01, atom= 111\n", + "Step= 611, Dmax= 1.0e-02 nm, Epot= -4.57468e+04 Fmax= 2.21624e+02, atom= 626\n", + "Step= 612, Dmax= 1.2e-02 nm, Epot= -4.57502e+04 Fmax= 9.43645e+01, atom= 626\n", + "Step= 614, Dmax= 7.4e-03 nm, Epot= -4.57512e+04 Fmax= 7.85514e+01, atom= 626\n", + "Step= 615, Dmax= 8.9e-03 nm, Epot= -4.57519e+04 Fmax= 1.32988e+02, atom= 626\n", + "Step= 616, Dmax= 1.1e-02 nm, Epot= -4.57530e+04 Fmax= 1.19382e+02, atom= 626\n", + "Step= 618, Dmax= 6.4e-03 nm, Epot= -4.57544e+04 Fmax= 2.94811e+01, atom= 626\n", + "Step= 619, Dmax= 7.7e-03 nm, Epot= -4.57556e+04 Fmax= 1.67790e+02, atom= 626\n", + "Step= 620, Dmax= 9.2e-03 nm, Epot= -4.57579e+04 Fmax= 5.88097e+01, atom= 626\n", + "Step= 622, Dmax= 5.5e-03 nm, Epot= -4.57589e+04 Fmax= 7.25233e+01, atom= 626\n", + "Step= 623, Dmax= 6.7e-03 nm, Epot= -4.57598e+04 Fmax= 8.45653e+01, atom= 626\n", + "Step= 624, Dmax= 8.0e-03 nm, Epot= -4.57606e+04 Fmax= 1.04557e+02, atom= 626\n", + "Step= 625, Dmax= 9.6e-03 nm, Epot= -4.57614e+04 Fmax= 1.23277e+02, atom= 626\n", + "Step= 626, Dmax= 1.2e-02 nm, Epot= -4.57620e+04 Fmax= 1.48313e+02, atom= 626\n", + "Step= 627, Dmax= 1.4e-02 nm, Epot= -4.57623e+04 Fmax= 1.83356e+02, atom= 626\n", + "Step= 628, Dmax= 1.7e-02 nm, Epot= -4.57627e+04 Fmax= 2.06961e+02, atom= 626\n", + "Step= 630, Dmax= 9.9e-03 nm, Epot= -4.57658e+04 Fmax= 3.36618e+01, atom= 111\n", + "Step= 631, Dmax= 1.2e-02 nm, Epot= -4.57661e+04 Fmax= 2.32675e+02, atom= 626\n", + "Step= 632, Dmax= 1.4e-02 nm, Epot= -4.57693e+04 Fmax= 1.43688e+02, atom= 626\n", + "Step= 634, Dmax= 8.6e-03 nm, Epot= -4.57709e+04 Fmax= 5.70110e+01, atom= 626\n", + "Step= 636, Dmax= 5.2e-03 nm, Epot= -4.57718e+04 Fmax= 6.27797e+01, atom= 626\n", + "Step= 637, Dmax= 6.2e-03 nm, Epot= -4.57727e+04 Fmax= 8.34530e+01, atom= 626\n", + "Step= 638, Dmax= 7.4e-03 nm, Epot= -4.57735e+04 Fmax= 9.19966e+01, atom= 626\n", + "Step= 639, Dmax= 8.9e-03 nm, Epot= -4.57742e+04 Fmax= 1.18256e+02, atom= 626\n", + "Step= 640, Dmax= 1.1e-02 nm, Epot= -4.57749e+04 Fmax= 1.36731e+02, atom= 626\n", + "Step= 641, Dmax= 1.3e-02 nm, Epot= -4.57753e+04 Fmax= 1.65361e+02, atom= 626\n", + "Step= 642, Dmax= 1.5e-02 nm, Epot= -4.57754e+04 Fmax= 2.05899e+02, atom= 626\n", + "Step= 643, Dmax= 1.8e-02 nm, Epot= -4.57756e+04 Fmax= 2.28102e+02, atom= 626\n", + "Step= 645, Dmax= 1.1e-02 nm, Epot= -4.57794e+04 Fmax= 4.02938e+01, atom= 111\n", + "Step= 647, Dmax= 6.6e-03 nm, Epot= -4.57805e+04 Fmax= 1.02959e+02, atom= 626\n", + "Step= 648, Dmax= 8.0e-03 nm, Epot= -4.57815e+04 Fmax= 9.19483e+01, atom= 626\n", + "Step= 649, Dmax= 9.6e-03 nm, Epot= -4.57820e+04 Fmax= 1.32794e+02, atom= 626\n", + "Step= 650, Dmax= 1.1e-02 nm, Epot= -4.57827e+04 Fmax= 1.41105e+02, atom= 626\n", + "Step= 651, Dmax= 1.4e-02 nm, Epot= -4.57829e+04 Fmax= 1.82665e+02, atom= 626\n", + "Step= 652, Dmax= 1.7e-02 nm, Epot= -4.57830e+04 Fmax= 2.16710e+02, atom= 626\n", + "Step= 654, Dmax= 9.9e-03 nm, Epot= -4.57864e+04 Fmax= 2.30861e+01, atom= 339\n", + "Step= 655, Dmax= 1.2e-02 nm, Epot= -4.57890e+04 Fmax= 2.47514e+02, atom= 339\n", + "Step= 656, Dmax= 1.4e-02 nm, Epot= -4.57916e+04 Fmax= 9.66893e+01, atom= 339\n", + "Step= 658, Dmax= 8.6e-03 nm, Epot= -4.57924e+04 Fmax= 1.12369e+02, atom= 339\n", + "Step= 659, Dmax= 1.0e-02 nm, Epot= -4.57930e+04 Fmax= 1.27581e+02, atom= 626\n", + "Step= 660, Dmax= 1.2e-02 nm, Epot= -4.57933e+04 Fmax= 1.70183e+02, atom= 339\n", + "Step= 661, Dmax= 1.5e-02 nm, Epot= -4.57939e+04 Fmax= 1.76601e+02, atom= 339\n", + "Step= 663, Dmax= 8.9e-03 nm, Epot= -4.57963e+04 Fmax= 3.23171e+01, atom= 111\n", + "Step= 665, Dmax= 5.3e-03 nm, Epot= -4.57974e+04 Fmax= 9.66383e+01, atom= 339\n", + "Step= 666, Dmax= 6.4e-03 nm, Epot= -4.57985e+04 Fmax= 5.82051e+01, atom= 626\n", + "Step= 667, Dmax= 7.7e-03 nm, Epot= -4.57991e+04 Fmax= 1.21677e+02, atom= 339\n", + "Step= 668, Dmax= 9.2e-03 nm, Epot= -4.58002e+04 Fmax= 9.81286e+01, atom= 339\n", + "Step= 669, Dmax= 1.1e-02 nm, Epot= -4.58003e+04 Fmax= 1.62097e+02, atom= 339\n", + "Step= 670, Dmax= 1.3e-02 nm, Epot= -4.58012e+04 Fmax= 1.57590e+02, atom= 339\n", + "Step= 672, Dmax= 8.0e-03 nm, Epot= -4.58033e+04 Fmax= 3.24485e+01, atom= 339\n", + "Step= 673, Dmax= 9.6e-03 nm, Epot= -4.58044e+04 Fmax= 1.91130e+02, atom= 339\n", + "Step= 674, Dmax= 1.1e-02 nm, Epot= -4.58066e+04 Fmax= 8.07609e+01, atom= 339\n", + "Step= 676, Dmax= 6.9e-03 nm, Epot= -4.58074e+04 Fmax= 7.90443e+01, atom= 339\n", + "Step= 677, Dmax= 8.3e-03 nm, Epot= -4.58080e+04 Fmax= 1.14352e+02, atom= 339\n", + "Step= 678, Dmax= 9.9e-03 nm, Epot= -4.58088e+04 Fmax= 1.21477e+02, atom= 339\n", + "Step= 679, Dmax= 1.2e-02 nm, Epot= -4.58091e+04 Fmax= 1.56905e+02, atom= 339\n", + "Step= 680, Dmax= 1.4e-02 nm, Epot= -4.58095e+04 Fmax= 1.86347e+02, atom= 339\n", + "Step= 681, Dmax= 1.7e-02 nm, Epot= -4.58096e+04 Fmax= 2.13906e+02, atom= 339\n", + "Step= 683, Dmax= 1.0e-02 nm, Epot= -4.58130e+04 Fmax= 3.28962e+01, atom= 111\n", + "Step= 685, Dmax= 6.2e-03 nm, Epot= -4.58142e+04 Fmax= 1.00185e+02, atom= 339\n", + "Step= 686, Dmax= 7.4e-03 nm, Epot= -4.58153e+04 Fmax= 8.16074e+01, atom= 339\n", + "Step= 687, Dmax= 8.9e-03 nm, Epot= -4.58158e+04 Fmax= 1.25340e+02, atom= 339\n", + "Step= 688, Dmax= 1.1e-02 nm, Epot= -4.58166e+04 Fmax= 1.28269e+02, atom= 339\n", + "Step= 689, Dmax= 1.3e-02 nm, Epot= -4.58168e+04 Fmax= 1.70713e+02, atom= 339\n", + "Step= 690, Dmax= 1.5e-02 nm, Epot= -4.58171e+04 Fmax= 1.98108e+02, atom= 339\n", + "Step= 692, Dmax= 9.2e-03 nm, Epot= -4.58200e+04 Fmax= 2.29123e+01, atom= 339\n", + "Step= 693, Dmax= 1.1e-02 nm, Epot= -4.58226e+04 Fmax= 2.23666e+02, atom= 339\n", + "Step= 694, Dmax= 1.3e-02 nm, Epot= -4.58249e+04 Fmax= 9.22479e+01, atom= 339\n", + "Step= 696, Dmax= 7.9e-03 nm, Epot= -4.58257e+04 Fmax= 9.87011e+01, atom= 339\n", + "Step= 697, Dmax= 9.5e-03 nm, Epot= -4.58264e+04 Fmax= 1.22014e+02, atom= 339\n", + "Step= 698, Dmax= 1.1e-02 nm, Epot= -4.58268e+04 Fmax= 1.51478e+02, atom= 339\n", + "Step= 699, Dmax= 1.4e-02 nm, Epot= -4.58274e+04 Fmax= 1.68389e+02, atom= 339\n", + "Step= 701, Dmax= 8.2e-03 nm, Epot= -4.58296e+04 Fmax= 2.49104e+01, atom= 111\n", + "Step= 702, Dmax= 9.9e-03 nm, Epot= -4.58302e+04 Fmax= 2.22306e+02, atom= 339\n", + "Step= 703, Dmax= 1.2e-02 nm, Epot= -4.58338e+04 Fmax= 8.38243e+01, atom= 339\n", + "Step= 705, Dmax= 7.1e-03 nm, Epot= -4.58347e+04 Fmax= 7.97399e+01, atom= 339\n", + "Step= 706, Dmax= 8.5e-03 nm, Epot= -4.58353e+04 Fmax= 1.22699e+02, atom= 339\n", + "Step= 707, Dmax= 1.0e-02 nm, Epot= -4.58362e+04 Fmax= 1.16140e+02, atom= 339\n", + "Step= 708, Dmax= 1.2e-02 nm, Epot= -4.58362e+04 Fmax= 1.77221e+02, atom= 339\n", + "Step= 709, Dmax= 1.5e-02 nm, Epot= -4.58372e+04 Fmax= 1.65875e+02, atom= 339\n", + "Step= 711, Dmax= 8.9e-03 nm, Epot= -4.58394e+04 Fmax= 3.68963e+01, atom= 339\n", + "Step= 713, Dmax= 5.3e-03 nm, Epot= -4.58404e+04 Fmax= 9.72060e+01, atom= 339\n", + "Step= 714, Dmax= 6.4e-03 nm, Epot= -4.58415e+04 Fmax= 5.42322e+01, atom= 339\n", + "Step= 715, Dmax= 7.7e-03 nm, Epot= -4.58422e+04 Fmax= 1.25504e+02, atom= 339\n", + "Step= 716, Dmax= 9.2e-03 nm, Epot= -4.58434e+04 Fmax= 9.14520e+01, atom= 339\n", + "Step= 717, Dmax= 1.1e-02 nm, Epot= -4.58435e+04 Fmax= 1.66624e+02, atom= 339\n", + "Step= 718, Dmax= 1.3e-02 nm, Epot= -4.58447e+04 Fmax= 1.48350e+02, atom= 339\n", + "Step= 720, Dmax= 7.9e-03 nm, Epot= -4.58466e+04 Fmax= 3.86064e+01, atom= 339\n", + "Step= 721, Dmax= 9.5e-03 nm, Epot= -4.58475e+04 Fmax= 1.82197e+02, atom= 339\n", + "Step= 722, Dmax= 1.1e-02 nm, Epot= -4.58495e+04 Fmax= 8.70904e+01, atom= 339\n", + "Step= 724, Dmax= 6.9e-03 nm, Epot= -4.58505e+04 Fmax= 7.01013e+01, atom= 339\n", + "Step= 725, Dmax= 8.2e-03 nm, Epot= -4.58512e+04 Fmax= 1.22960e+02, atom= 339\n", + "Step= 726, Dmax= 9.9e-03 nm, Epot= -4.58523e+04 Fmax= 1.09954e+02, atom= 339\n", + "Step= 727, Dmax= 1.2e-02 nm, Epot= -4.58525e+04 Fmax= 1.65851e+02, atom= 339\n", + "Step= 728, Dmax= 1.4e-02 nm, Epot= -4.58533e+04 Fmax= 1.72371e+02, atom= 339\n", + "Step= 730, Dmax= 8.5e-03 nm, Epot= -4.58557e+04 Fmax= 2.92063e+01, atom= 626\n", + "Step= 731, Dmax= 1.0e-02 nm, Epot= -4.58575e+04 Fmax= 2.06424e+02, atom= 339\n", + "Step= 732, Dmax= 1.2e-02 nm, Epot= -4.58599e+04 Fmax= 8.49054e+01, atom= 339\n", + "Step= 734, Dmax= 7.4e-03 nm, Epot= -4.58609e+04 Fmax= 8.57352e+01, atom= 339\n", + "Step= 735, Dmax= 8.8e-03 nm, Epot= -4.58617e+04 Fmax= 1.18904e+02, atom= 339\n", + "Step= 736, Dmax= 1.1e-02 nm, Epot= -4.58626e+04 Fmax= 1.30971e+02, atom= 339\n", + "Step= 737, Dmax= 1.3e-02 nm, Epot= -4.58631e+04 Fmax= 1.64207e+02, atom= 339\n", + "Step= 738, Dmax= 1.5e-02 nm, Epot= -4.58634e+04 Fmax= 1.99393e+02, atom= 339\n", + "Step= 739, Dmax= 1.8e-02 nm, Epot= -4.58637e+04 Fmax= 2.24656e+02, atom= 339\n", + "Step= 741, Dmax= 1.1e-02 nm, Epot= -4.58674e+04 Fmax= 3.67078e+01, atom= 373\n", + "Step= 743, Dmax= 6.6e-03 nm, Epot= -4.58688e+04 Fmax= 1.08037e+02, atom= 339\n", + "Step= 744, Dmax= 7.9e-03 nm, Epot= -4.58701e+04 Fmax= 8.31847e+01, atom= 339\n", + "Step= 745, Dmax= 9.5e-03 nm, Epot= -4.58708e+04 Fmax= 1.36275e+02, atom= 339\n", + "Step= 746, Dmax= 1.1e-02 nm, Epot= -4.58718e+04 Fmax= 1.31440e+02, atom= 339\n", + "Step= 747, Dmax= 1.4e-02 nm, Epot= -4.58720e+04 Fmax= 1.86017e+02, atom= 339\n", + "Step= 748, Dmax= 1.6e-02 nm, Epot= -4.58727e+04 Fmax= 2.04077e+02, atom= 339\n", + "Step= 750, Dmax= 9.9e-03 nm, Epot= -4.58758e+04 Fmax= 3.01696e+01, atom= 626\n", + "Step= 751, Dmax= 1.2e-02 nm, Epot= -4.58782e+04 Fmax= 2.29559e+02, atom= 626\n", + "Step= 752, Dmax= 1.4e-02 nm, Epot= -4.58808e+04 Fmax= 1.07844e+02, atom= 339\n", + "Step= 754, Dmax= 8.5e-03 nm, Epot= -4.58820e+04 Fmax= 8.79604e+01, atom= 339\n", + "Step= 755, Dmax= 1.0e-02 nm, Epot= -4.58826e+04 Fmax= 1.49108e+02, atom= 339\n", + "Step= 756, Dmax= 1.2e-02 nm, Epot= -4.58838e+04 Fmax= 1.38957e+02, atom= 339\n", + "Step= 757, Dmax= 1.5e-02 nm, Epot= -4.58838e+04 Fmax= 2.02099e+02, atom= 339\n", + "Step= 758, Dmax= 1.8e-02 nm, Epot= -4.58845e+04 Fmax= 2.17486e+02, atom= 339\n", + "Step= 760, Dmax= 1.1e-02 nm, Epot= -4.58880e+04 Fmax= 3.34163e+01, atom= 626\n", + "Step= 761, Dmax= 1.3e-02 nm, Epot= -4.58900e+04 Fmax= 2.47808e+02, atom= 626\n", + "Step= 762, Dmax= 1.5e-02 nm, Epot= -4.58930e+04 Fmax= 1.16214e+02, atom= 339\n", + "Step= 764, Dmax= 9.2e-03 nm, Epot= -4.58942e+04 Fmax= 9.36903e+01, atom= 339\n", + "Step= 765, Dmax= 1.1e-02 nm, Epot= -4.58947e+04 Fmax= 1.61052e+02, atom= 339\n", + "Step= 766, Dmax= 1.3e-02 nm, Epot= -4.58960e+04 Fmax= 1.47897e+02, atom= 339\n", + "Step= 768, Dmax= 7.9e-03 nm, Epot= -4.58980e+04 Fmax= 3.58704e+01, atom= 626\n", + "Step= 769, Dmax= 9.5e-03 nm, Epot= -4.58997e+04 Fmax= 1.83300e+02, atom= 339\n", + "Step= 770, Dmax= 1.1e-02 nm, Epot= -4.59019e+04 Fmax= 8.29662e+01, atom= 339\n", + "Step= 772, Dmax= 6.8e-03 nm, Epot= -4.59031e+04 Fmax= 7.23602e+01, atom= 339\n", + "Step= 773, Dmax= 8.2e-03 nm, Epot= -4.59041e+04 Fmax= 1.17845e+02, atom= 339\n", + "Step= 774, Dmax= 9.8e-03 nm, Epot= -4.59053e+04 Fmax= 1.11226e+02, atom= 339\n", + "Step= 775, Dmax= 1.2e-02 nm, Epot= -4.59059e+04 Fmax= 1.61287e+02, atom= 339\n", + "Step= 776, Dmax= 1.4e-02 nm, Epot= -4.59068e+04 Fmax= 1.70512e+02, atom= 339\n", + "Step= 777, Dmax= 1.7e-02 nm, Epot= -4.59069e+04 Fmax= 2.21020e+02, atom= 339\n", + "Step= 778, Dmax= 2.0e-02 nm, Epot= -4.59070e+04 Fmax= 2.63265e+02, atom= 339\n", + "Step= 780, Dmax= 1.2e-02 nm, Epot= -4.59118e+04 Fmax= 2.87628e+01, atom= 626\n", + "Step= 781, Dmax= 1.5e-02 nm, Epot= -4.59154e+04 Fmax= 2.75397e+02, atom= 626\n", + "Step= 782, Dmax= 1.8e-02 nm, Epot= -4.59182e+04 Fmax= 1.44366e+02, atom= 339\n", + "Step= 784, Dmax= 1.1e-02 nm, Epot= -4.59197e+04 Fmax= 1.03991e+02, atom= 339\n", + "Step= 785, Dmax= 1.3e-02 nm, Epot= -4.59198e+04 Fmax= 1.88353e+02, atom= 339\n", + "Step= 786, Dmax= 1.5e-02 nm, Epot= -4.59213e+04 Fmax= 1.68242e+02, atom= 339\n", + "Step= 788, Dmax= 9.1e-03 nm, Epot= -4.59236e+04 Fmax= 4.25005e+01, atom= 626\n", + "Step= 789, Dmax= 1.1e-02 nm, Epot= -4.59247e+04 Fmax= 2.08891e+02, atom= 339\n", + "Step= 790, Dmax= 1.3e-02 nm, Epot= -4.59273e+04 Fmax= 9.82721e+01, atom= 339\n", + "Step= 792, Dmax= 7.9e-03 nm, Epot= -4.59285e+04 Fmax= 7.88287e+01, atom= 339\n", + "Step= 793, Dmax= 9.5e-03 nm, Epot= -4.59292e+04 Fmax= 1.40228e+02, atom= 339\n", + "Step= 794, Dmax= 1.1e-02 nm, Epot= -4.59305e+04 Fmax= 1.23526e+02, atom= 339\n", + "Step= 795, Dmax= 1.4e-02 nm, Epot= -4.59306e+04 Fmax= 1.90196e+02, atom= 339\n", + "Step= 796, Dmax= 1.6e-02 nm, Epot= -4.59316e+04 Fmax= 1.92276e+02, atom= 339\n", + "Step= 798, Dmax= 9.8e-03 nm, Epot= -4.59345e+04 Fmax= 3.59415e+01, atom= 626\n", + "Step= 799, Dmax= 1.2e-02 nm, Epot= -4.59361e+04 Fmax= 2.22986e+02, atom= 626\n", + "Step= 800, Dmax= 1.4e-02 nm, Epot= -4.59388e+04 Fmax= 1.08835e+02, atom= 339\n", + "Step= 802, Dmax= 8.5e-03 nm, Epot= -4.59400e+04 Fmax= 8.22214e+01, atom= 339\n", + "Step= 803, Dmax= 1.0e-02 nm, Epot= -4.59405e+04 Fmax= 1.52607e+02, atom= 339\n", + "Step= 804, Dmax= 1.2e-02 nm, Epot= -4.59419e+04 Fmax= 1.30530e+02, atom= 339\n", + "Step= 806, Dmax= 7.3e-03 nm, Epot= -4.59436e+04 Fmax= 3.69766e+01, atom= 339\n", + "Step= 807, Dmax= 8.8e-03 nm, Epot= -4.59450e+04 Fmax= 1.64574e+02, atom= 339\n", + "Step= 808, Dmax= 1.1e-02 nm, Epot= -4.59470e+04 Fmax= 7.84499e+01, atom= 339\n", + "Step= 810, Dmax= 6.3e-03 nm, Epot= -4.59481e+04 Fmax= 6.38636e+01, atom= 339\n", + "Step= 811, Dmax= 7.6e-03 nm, Epot= -4.59490e+04 Fmax= 1.10600e+02, atom= 339\n", + "Step= 812, Dmax= 9.1e-03 nm, Epot= -4.59502e+04 Fmax= 9.94042e+01, atom= 339\n", + "Step= 813, Dmax= 1.1e-02 nm, Epot= -4.59508e+04 Fmax= 1.50806e+02, atom= 339\n", + "Step= 814, Dmax= 1.3e-02 nm, Epot= -4.59518e+04 Fmax= 1.53324e+02, atom= 339\n", + "Step= 815, Dmax= 1.6e-02 nm, Epot= -4.59519e+04 Fmax= 2.06270e+02, atom= 339\n", + "Step= 816, Dmax= 1.9e-02 nm, Epot= -4.59522e+04 Fmax= 2.35618e+02, atom= 339\n", + "Step= 818, Dmax= 1.1e-02 nm, Epot= -4.59562e+04 Fmax= 3.07404e+01, atom= 626\n", + "Step= 819, Dmax= 1.4e-02 nm, Epot= -4.59589e+04 Fmax= 2.49983e+02, atom= 626\n", + "Step= 820, Dmax= 1.6e-02 nm, Epot= -4.59615e+04 Fmax= 1.31232e+02, atom= 339\n", + "Step= 822, Dmax= 9.8e-03 nm, Epot= -4.59629e+04 Fmax= 9.17377e+01, atom= 339\n", + "Step= 823, Dmax= 1.2e-02 nm, Epot= -4.59630e+04 Fmax= 1.78002e+02, atom= 339\n", + "Step= 824, Dmax= 1.4e-02 nm, Epot= -4.59645e+04 Fmax= 1.47893e+02, atom= 339\n", + "Step= 826, Dmax= 8.5e-03 nm, Epot= -4.59665e+04 Fmax= 4.37481e+01, atom= 626\n", + "Step= 827, Dmax= 1.0e-02 nm, Epot= -4.59674e+04 Fmax= 1.88920e+02, atom= 339\n", + "Step= 828, Dmax= 1.2e-02 nm, Epot= -4.59697e+04 Fmax= 9.13859e+01, atom= 339\n", + "Step= 830, Dmax= 7.3e-03 nm, Epot= -4.59708e+04 Fmax= 7.08268e+01, atom= 339\n", + "Step= 831, Dmax= 8.8e-03 nm, Epot= -4.59716e+04 Fmax= 1.30459e+02, atom= 339\n", + "Step= 832, Dmax= 1.1e-02 nm, Epot= -4.59729e+04 Fmax= 1.10408e+02, atom= 339\n", + "Step= 833, Dmax= 1.3e-02 nm, Epot= -4.59731e+04 Fmax= 1.76787e+02, atom= 339\n", + "Step= 834, Dmax= 1.5e-02 nm, Epot= -4.59743e+04 Fmax= 1.72232e+02, atom= 339\n", + "Step= 836, Dmax= 9.1e-03 nm, Epot= -4.59767e+04 Fmax= 3.56087e+01, atom= 626\n", + "Step= 837, Dmax= 1.1e-02 nm, Epot= -4.59783e+04 Fmax= 2.02562e+02, atom= 339\n", + "Step= 838, Dmax= 1.3e-02 nm, Epot= -4.59807e+04 Fmax= 1.00461e+02, atom= 339\n", + "Step= 840, Dmax= 7.9e-03 nm, Epot= -4.59820e+04 Fmax= 7.41119e+01, atom= 339\n", + "Step= 841, Dmax= 9.4e-03 nm, Epot= -4.59826e+04 Fmax= 1.40962e+02, atom= 339\n", + "Step= 842, Dmax= 1.1e-02 nm, Epot= -4.59840e+04 Fmax= 1.17473e+02, atom= 339\n", + "Step= 843, Dmax= 1.4e-02 nm, Epot= -4.59841e+04 Fmax= 1.90774e+02, atom= 339\n", + "Step= 844, Dmax= 1.6e-02 nm, Epot= -4.59852e+04 Fmax= 1.83520e+02, atom= 339\n", + "Step= 846, Dmax= 9.8e-03 nm, Epot= -4.59879e+04 Fmax= 3.89524e+01, atom= 626\n", + "Step= 847, Dmax= 1.2e-02 nm, Epot= -4.59892e+04 Fmax= 2.14554e+02, atom= 626\n", + "Step= 848, Dmax= 1.4e-02 nm, Epot= -4.59918e+04 Fmax= 1.09660e+02, atom= 339\n", + "Step= 850, Dmax= 8.5e-03 nm, Epot= -4.59931e+04 Fmax= 7.67259e+01, atom= 339\n", + "Step= 851, Dmax= 1.0e-02 nm, Epot= -4.59936e+04 Fmax= 1.54610e+02, atom= 339\n", + "Step= 852, Dmax= 1.2e-02 nm, Epot= -4.59951e+04 Fmax= 1.22581e+02, atom= 339\n", + "Step= 854, Dmax= 7.3e-03 nm, Epot= -4.59967e+04 Fmax= 4.02329e+01, atom= 339\n", + "Step= 855, Dmax= 8.8e-03 nm, Epot= -4.59980e+04 Fmax= 1.57835e+02, atom= 339\n", + "Step= 856, Dmax= 1.1e-02 nm, Epot= -4.59999e+04 Fmax= 7.94969e+01, atom= 339\n", + "Step= 858, Dmax= 6.3e-03 nm, Epot= -4.60010e+04 Fmax= 5.93191e+01, atom= 339\n", + "Step= 859, Dmax= 7.6e-03 nm, Epot= -4.60020e+04 Fmax= 1.12260e+02, atom= 339\n", + "Step= 860, Dmax= 9.1e-03 nm, Epot= -4.60032e+04 Fmax= 9.29688e+01, atom= 339\n", + "Step= 861, Dmax= 1.1e-02 nm, Epot= -4.60037e+04 Fmax= 1.52243e+02, atom= 339\n", + "Step= 862, Dmax= 1.3e-02 nm, Epot= -4.60049e+04 Fmax= 1.44542e+02, atom= 339\n", + "Step= 864, Dmax= 7.9e-03 nm, Epot= -4.60067e+04 Fmax= 3.12378e+01, atom= 626\n", + "Step= 865, Dmax= 9.4e-03 nm, Epot= -4.60086e+04 Fmax= 1.74690e+02, atom= 339\n", + "Step= 866, Dmax= 1.1e-02 nm, Epot= -4.60107e+04 Fmax= 8.15345e+01, atom= 339\n", + "Step= 868, Dmax= 6.8e-03 nm, Epot= -4.60118e+04 Fmax= 6.76013e+01, atom= 339\n", + "Step= 869, Dmax= 8.1e-03 nm, Epot= -4.60127e+04 Fmax= 1.15008e+02, atom= 339\n", + "Step= 870, Dmax= 9.8e-03 nm, Epot= -4.60138e+04 Fmax= 1.04545e+02, atom= 339\n", + "Step= 871, Dmax= 1.2e-02 nm, Epot= -4.60143e+04 Fmax= 1.57190e+02, atom= 339\n", + "Step= 872, Dmax= 1.4e-02 nm, Epot= -4.60153e+04 Fmax= 1.59444e+02, atom= 339\n", + "Step= 874, Dmax= 8.4e-03 nm, Epot= -4.60175e+04 Fmax= 2.95869e+01, atom= 626\n", + "Step= 875, Dmax= 1.0e-02 nm, Epot= -4.60195e+04 Fmax= 1.82758e+02, atom= 626\n", + "Step= 876, Dmax= 1.2e-02 nm, Epot= -4.60217e+04 Fmax= 9.26096e+01, atom= 339\n", + "Step= 878, Dmax= 7.3e-03 nm, Epot= -4.60228e+04 Fmax= 6.74876e+01, atom= 339\n", + "Step= 879, Dmax= 8.8e-03 nm, Epot= -4.60236e+04 Fmax= 1.28510e+02, atom= 339\n", + "Step= 880, Dmax= 1.1e-02 nm, Epot= -4.60248e+04 Fmax= 1.06742e+02, atom= 339\n", + "Step= 881, Dmax= 1.3e-02 nm, Epot= -4.60250e+04 Fmax= 1.73983e+02, atom= 339\n", + "Step= 882, Dmax= 1.5e-02 nm, Epot= -4.60261e+04 Fmax= 1.64498e+02, atom= 339\n", + "Step= 884, Dmax= 9.1e-03 nm, Epot= -4.60284e+04 Fmax= 3.65172e+01, atom= 626\n", + "Step= 885, Dmax= 1.1e-02 nm, Epot= -4.60296e+04 Fmax= 1.93786e+02, atom= 626\n", + "Step= 886, Dmax= 1.3e-02 nm, Epot= -4.60320e+04 Fmax= 1.00589e+02, atom= 339\n", + "Step= 888, Dmax= 7.8e-03 nm, Epot= -4.60332e+04 Fmax= 6.96189e+01, atom= 339\n", + "Step= 889, Dmax= 9.4e-03 nm, Epot= -4.60338e+04 Fmax= 1.40895e+02, atom= 339\n", + "Step= 890, Dmax= 1.1e-02 nm, Epot= -4.60351e+04 Fmax= 1.09929e+02, atom= 339\n", + "Step= 892, Dmax= 6.8e-03 nm, Epot= -4.60365e+04 Fmax= 3.78470e+01, atom= 339\n", + "Step= 893, Dmax= 8.1e-03 nm, Epot= -4.60377e+04 Fmax= 1.40660e+02, atom= 339\n", + "Step= 894, Dmax= 9.8e-03 nm, Epot= -4.60393e+04 Fmax= 7.44084e+01, atom= 339\n", + "Step= 896, Dmax= 5.9e-03 nm, Epot= -4.60404e+04 Fmax= 5.29986e+01, atom= 339\n", + "Step= 897, Dmax= 7.0e-03 nm, Epot= -4.60413e+04 Fmax= 1.03341e+02, atom= 339\n", + "Step= 898, Dmax= 8.4e-03 nm, Epot= -4.60424e+04 Fmax= 8.34452e+01, atom= 339\n", + "Step= 899, Dmax= 1.0e-02 nm, Epot= -4.60430e+04 Fmax= 1.40299e+02, atom= 339\n", + "Step= 900, Dmax= 1.2e-02 nm, Epot= -4.60441e+04 Fmax= 1.27627e+02, atom= 339\n", + "Step= 902, Dmax= 7.3e-03 nm, Epot= -4.60457e+04 Fmax= 3.10242e+01, atom= 626\n", + "Step= 903, Dmax= 8.7e-03 nm, Epot= -4.60472e+04 Fmax= 1.59598e+02, atom= 339\n", + "Step= 904, Dmax= 1.0e-02 nm, Epot= -4.60491e+04 Fmax= 7.32902e+01, atom= 339\n", + "Step= 906, Dmax= 6.3e-03 nm, Epot= -4.60501e+04 Fmax= 6.22260e+01, atom= 339\n", + "Step= 907, Dmax= 7.6e-03 nm, Epot= -4.60509e+04 Fmax= 1.04430e+02, atom= 339\n", + "Step= 908, Dmax= 9.1e-03 nm, Epot= -4.60519e+04 Fmax= 9.36935e+01, atom= 339\n", + "Step= 909, Dmax= 1.1e-02 nm, Epot= -4.60524e+04 Fmax= 1.45083e+02, atom= 339\n", + "Step= 910, Dmax= 1.3e-02 nm, Epot= -4.60533e+04 Fmax= 1.42734e+02, atom= 339\n", + "Step= 912, Dmax= 7.8e-03 nm, Epot= -4.60551e+04 Fmax= 2.79819e+01, atom= 626\n", + "Step= 913, Dmax= 9.4e-03 nm, Epot= -4.60567e+04 Fmax= 1.69572e+02, atom= 339\n", + "Step= 914, Dmax= 1.1e-02 nm, Epot= -4.60587e+04 Fmax= 8.09347e+01, atom= 339\n", + "Step= 916, Dmax= 6.8e-03 nm, Epot= -4.60596e+04 Fmax= 6.40327e+01, atom= 339\n", + "Step= 917, Dmax= 8.1e-03 nm, Epot= -4.60603e+04 Fmax= 1.14264e+02, atom= 339\n", + "Step= 918, Dmax= 9.7e-03 nm, Epot= -4.60613e+04 Fmax= 9.81419e+01, atom= 339\n", + "Step= 919, Dmax= 1.2e-02 nm, Epot= -4.60614e+04 Fmax= 1.57401e+02, atom= 339\n", + "Step= 920, Dmax= 1.4e-02 nm, Epot= -4.60623e+04 Fmax= 1.50803e+02, atom= 339\n", + "Step= 922, Dmax= 8.4e-03 nm, Epot= -4.60642e+04 Fmax= 3.15662e+01, atom= 626\n", + "Step= 923, Dmax= 1.0e-02 nm, Epot= -4.60652e+04 Fmax= 1.80039e+02, atom= 339\n", + "Step= 924, Dmax= 1.2e-02 nm, Epot= -4.60673e+04 Fmax= 8.82780e+01, atom= 339\n", + "Step= 926, Dmax= 7.3e-03 nm, Epot= -4.60682e+04 Fmax= 6.53041e+01, atom= 339\n", + "Step= 927, Dmax= 8.7e-03 nm, Epot= -4.60686e+04 Fmax= 1.26425e+02, atom= 339\n", + "Step= 928, Dmax= 1.0e-02 nm, Epot= -4.60697e+04 Fmax= 1.01643e+02, atom= 339\n", + "Step= 930, Dmax= 6.3e-03 nm, Epot= -4.60708e+04 Fmax= 3.34565e+01, atom= 339\n", + "Step= 931, Dmax= 7.5e-03 nm, Epot= -4.60716e+04 Fmax= 1.28651e+02, atom= 339\n", + "Step= 932, Dmax= 9.1e-03 nm, Epot= -4.60731e+04 Fmax= 6.67952e+01, atom= 339\n", + "Step= 934, Dmax= 5.4e-03 nm, Epot= -4.60739e+04 Fmax= 4.89232e+01, atom= 339\n", + "Step= 935, Dmax= 6.5e-03 nm, Epot= -4.60745e+04 Fmax= 9.32006e+01, atom= 339\n", + "Step= 936, Dmax= 7.8e-03 nm, Epot= -4.60754e+04 Fmax= 7.53156e+01, atom= 339\n", + "Step= 937, Dmax= 9.4e-03 nm, Epot= -4.60754e+04 Fmax= 1.28261e+02, atom= 339\n", + "Step= 938, Dmax= 1.1e-02 nm, Epot= -4.60762e+04 Fmax= 1.16226e+02, atom= 339\n", + "Step= 940, Dmax= 6.8e-03 nm, Epot= -4.60780e+04 Fmax= 2.95041e+01, atom= 1368\n", + "Step= 942, Dmax= 4.1e-03 nm, Epot= -4.60788e+04 Fmax= 6.31746e+01, atom= 1368\n", + "Step= 943, Dmax= 4.9e-03 nm, Epot= -4.60796e+04 Fmax= 4.76729e+01, atom= 1368\n", + "Step= 944, Dmax= 5.8e-03 nm, Epot= -4.60802e+04 Fmax= 8.41276e+01, atom= 1368\n", + "Step= 945, Dmax= 7.0e-03 nm, Epot= -4.60810e+04 Fmax= 7.53131e+01, atom= 1368\n", + "Step= 946, Dmax= 8.4e-03 nm, Epot= -4.60814e+04 Fmax= 1.14408e+02, atom= 1368\n", + "Step= 947, Dmax= 1.0e-02 nm, Epot= -4.60821e+04 Fmax= 1.15662e+02, atom= 1368\n", + "Step= 948, Dmax= 1.2e-02 nm, Epot= -4.60822e+04 Fmax= 1.57248e+02, atom= 1368\n", + "Step= 949, Dmax= 1.5e-02 nm, Epot= -4.60828e+04 Fmax= 1.74987e+02, atom= 1368\n", + "Step= 951, Dmax= 8.7e-03 nm, Epot= -4.60848e+04 Fmax= 3.01782e+01, atom= 1345\n", + "Step= 952, Dmax= 1.0e-02 nm, Epot= -4.60855e+04 Fmax= 2.14247e+02, atom= 1368\n", + "Step= 953, Dmax= 1.3e-02 nm, Epot= -4.60876e+04 Fmax= 8.94970e+01, atom= 1368\n", + "Step= 955, Dmax= 7.5e-03 nm, Epot= -4.60883e+04 Fmax= 7.76314e+01, atom= 1368\n", + "Step= 956, Dmax= 9.0e-03 nm, Epot= -4.60887e+04 Fmax= 1.25467e+02, atom= 1368\n", + "Step= 957, Dmax= 1.1e-02 nm, Epot= -4.60894e+04 Fmax= 1.19966e+02, atom= 1368\n", + "Step= 959, Dmax= 6.5e-03 nm, Epot= -4.60905e+04 Fmax= 2.95166e+01, atom= 1368\n", + "Step= 960, Dmax= 7.8e-03 nm, Epot= -4.60914e+04 Fmax= 1.54612e+02, atom= 1368\n", + "Step= 961, Dmax= 9.4e-03 nm, Epot= -4.60927e+04 Fmax= 6.45018e+01, atom= 1368\n", + "Step= 963, Dmax= 5.6e-03 nm, Epot= -4.60933e+04 Fmax= 6.11630e+01, atom= 1368\n", + "Step= 964, Dmax= 6.7e-03 nm, Epot= -4.60939e+04 Fmax= 9.07986e+01, atom= 1368\n", + "Step= 965, Dmax= 8.1e-03 nm, Epot= -4.60945e+04 Fmax= 9.25017e+01, atom= 1368\n", + "Step= 966, Dmax= 9.7e-03 nm, Epot= -4.60949e+04 Fmax= 1.26024e+02, atom= 1368\n", + "Step= 967, Dmax= 1.2e-02 nm, Epot= -4.60954e+04 Fmax= 1.38783e+02, atom= 1368\n", + "Step= 968, Dmax= 1.4e-02 nm, Epot= -4.60955e+04 Fmax= 1.75522e+02, atom= 1368\n", + "Step= 969, Dmax= 1.7e-02 nm, Epot= -4.60957e+04 Fmax= 2.07413e+02, atom= 1368\n", + "Step= 971, Dmax= 1.0e-02 nm, Epot= -4.60980e+04 Fmax= 3.19811e+01, atom= 1345\n", + "Step= 972, Dmax= 1.2e-02 nm, Epot= -4.60984e+04 Fmax= 2.31645e+02, atom= 1368\n", + "Step= 973, Dmax= 1.5e-02 nm, Epot= -4.61004e+04 Fmax= 1.20309e+02, atom= 1368\n", + "Step= 975, Dmax= 8.7e-03 nm, Epot= -4.61013e+04 Fmax= 7.04173e+01, atom= 1368\n", + "Step= 977, Dmax= 5.2e-03 nm, Epot= -4.61019e+04 Fmax= 4.83563e+01, atom= 1368\n", + "Step= 978, Dmax= 6.3e-03 nm, Epot= -4.61025e+04 Fmax= 9.28116e+01, atom= 1368\n", + "Step= 979, Dmax= 7.5e-03 nm, Epot= -4.61032e+04 Fmax= 7.70792e+01, atom= 1368\n", + "Step= 980, Dmax= 9.0e-03 nm, Epot= -4.61035e+04 Fmax= 1.28397e+02, atom= 1368\n", + "Step= 981, Dmax= 1.1e-02 nm, Epot= -4.61042e+04 Fmax= 1.15731e+02, atom= 1368\n", + "Step= 983, Dmax= 6.5e-03 nm, Epot= -4.61052e+04 Fmax= 2.69529e+01, atom= 1368\n", + "Step= 984, Dmax= 7.8e-03 nm, Epot= -4.61059e+04 Fmax= 1.55765e+02, atom= 1368\n", + "Step= 985, Dmax= 9.4e-03 nm, Epot= -4.61074e+04 Fmax= 5.79249e+01, atom= 1368\n", + "Step= 987, Dmax= 5.6e-03 nm, Epot= -4.61079e+04 Fmax= 6.65819e+01, atom= 1368\n", + "Step= 988, Dmax= 6.7e-03 nm, Epot= -4.61084e+04 Fmax= 8.52191e+01, atom= 1368\n", + "Step= 989, Dmax= 8.1e-03 nm, Epot= -4.61090e+04 Fmax= 9.58728e+01, atom= 1368\n", + "Step= 990, Dmax= 9.7e-03 nm, Epot= -4.61093e+04 Fmax= 1.23232e+02, atom= 1368\n", + "Step= 991, Dmax= 1.2e-02 nm, Epot= -4.61097e+04 Fmax= 1.37459e+02, atom= 1368\n", + "Step= 992, Dmax= 1.4e-02 nm, Epot= -4.61098e+04 Fmax= 1.79358e+02, atom= 1368\n", + "Step= 993, Dmax= 1.7e-02 nm, Epot= -4.61099e+04 Fmax= 1.95544e+02, atom= 1368\n", + "Step= 995, Dmax= 1.0e-02 nm, Epot= -4.61122e+04 Fmax= 2.91625e+01, atom= 1076\n", + "Step= 996, Dmax= 1.2e-02 nm, Epot= -4.61123e+04 Fmax= 2.26608e+02, atom= 1368\n", + "Step= 997, Dmax= 1.4e-02 nm, Epot= -4.61145e+04 Fmax= 1.22948e+02, atom= 1368\n", + "Step= 999, Dmax= 8.7e-03 nm, Epot= -4.61154e+04 Fmax= 6.60313e+01, atom= 1368\n", + "Step= 1000, Dmax= 1.0e-02 nm, Epot= -4.61151e+04 Fmax= 1.79608e+02, atom= 1368\n", + "Energy minimization reached the maximum number of steps before the forces\n", + "reached the requested precision Fmax < 10.\n", + "\n", + "writing lowest energy coordinates.\n", + "\n", + "Back Off! I just backed up em.pdb to ./#em.pdb.1#\n", + "\n", + "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", + "Potential Energy = -4.6115398e+04\n", + "Maximum force = 6.6031342e+01 on atom 1368\n", + "Norm of force = 3.1664403e+00\n", + "\n", + "GROMACS reminds you: \"Everything's formed from particles\" (Van der Graaf Generator)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Naive you are if you believe life favours those who aren't naive.\" (Piet Hein)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] All files set up for a run time of 1000 ps (dt=0.01, nsteps=100000)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1087517089\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.132 nm, buffer size 0.032 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.108 nm, buffer size 0.008 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 1 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'struct': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.gro',\n", + " 'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top',\n", + " '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top']}" + ] + }, + "execution_count": 38, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from mdpow.equil import WaterSimulation\n", + "\n", + "sim = WaterSimulation(\n", + " molecule=\"BENZ\",\n", + " forcefield=MARTINI,\n", + " mdp={\n", + " \"energy_minimize\": str(EM_FILE.absolute()),\n", + " \"MD_relaxed\": str(EQ_FILE.absolute()),\n", + " \"MD_NPT\": str(EQ_FILE.absolute()),\n", + " \"MD_restrained\": str(RUN_FILE.absolute()),\n", + " },\n", + " distance=3.0,\n", + ")\n", + "sim.topology(str(BENZENE_ITP))\n", + "sim.solvate(struct=MARTINI_BENZENE, maxwarn=1)\n", + "sim.energy_minimize(maxwarn=1)\n", + "sim.MD_relaxed(runtime=1e3, dt=0.01)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We can execute `mdrun` using `GromacsWrapper`:" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 10 to 50, rlist from 1.107 to 1.268\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the GPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "100000 steps, 1000.0 ps (continuing from step 100000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 100000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.028 0.007 394.3\n", + " (ns/day) (hour/ns)\n", + "Performance: 120.539 0.199\n", + "\n", + "GROMACS reminds you: \"I have noticed a large, negative correlation between having a well-defined mission workload and concern for the Top500. It's almost like LINPACK is what you focus on when you don't know what to focus on.\" (Jeff Hammond)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + }, + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 39, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "r = gromacs.run.MDrunner(\n", + " dirname=sim.dirs[\"MD_relaxed\"],\n", + " deffnm=\"md\",\n", + " c=\"md.pdb\",\n", + " cpi=True,\n", + " v=True,\n", + ")\n", + "r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we do the same thing for a longer NPT run, with a longer timestep." + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.equil : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.gro').\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 't']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -t /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "Last frame -1 time 1000.000 \n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"This really is a pretty scene, could you ask your kid to smile please?\" (Joe Jackson)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] All files set up for a run time of 10000 ps (dt=0.02, nsteps=500000)\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1880144435\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.175 nm, buffer size 0.075 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.133 nm, buffer size 0.033 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "Reading Coordinates, Velocities and Box size from old trajectory\n", + "\n", + "Will read whole trajectory\n", + "\n", + "Using frame at t = 1000 ps\n", + "\n", + "Starting time for run is 0 ps\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 10 to 25, rlist from 1.133 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the GPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "500000 steps, 10000.0 ps (continuing from step 500000, 10000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 500000, remaining wall clock time: 0 s \n", + "NOTE: 19 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.053 0.013 397.2\n", + " (ns/day) (hour/ns)\n", + "Performance: 129.150 0.186\n", + "\n", + "GROMACS reminds you: \"This really is a pretty scene, could you ask your kid to smile please?\" (Joe Jackson)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + }, + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 40, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "sim.MD(\n", + " runtime=1e4, qscript=[\"local.sh\"], dt=0.02\n", + ")\n", + "\n", + "r = gromacs.run.MDrunner(\n", + " dirname=sim.dirs[\"MD_NPT\"], deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True\n", + ")\n", + "r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Finally, we can set up the thermodynamic integration files. The following will create several directories, one for each $\\lambda$ value:" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.gro').\n", + "/home/awsm/MDPOW/mdpow/fep.py:596: UserWarning: Directory 'FEP/water' already exists --- will overwrite existing files.\n", + " warnings.warn(wmsg)\n", + "mdpow.fep : WARNING Directory 'FEP/water' already exists --- will overwrite existing files.\n", + "mdpow.fep : INFO Solvation free energy calculation for molecule BENZ in solvent water.\n", + "mdpow.fep : INFO Base directory is '/home/awsm/MDPOW/doc/examples/martini'\n", + "mdpow.fep : INFO Using setup directories under 'FEP/water': {'coulomb': 'FEP/water/Coulomb', 'vdw': 'FEP/water/VDW'}\n", + "mdpow.fep : INFO Default checkpoint file is '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep'\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"It's Bicycle Repair Man !\" (Monty Python)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.25\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -176167043\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 2 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"And It Goes a Little Something Like This\" (Tag Team)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1878752383\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 2 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"And It Goes a Little Something Like This\" (Tag Team)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -279132165\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 2 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The easiest way to scale well is to have bad single-core performance\" (Blind Freddie)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 970913279\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 2 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The easiest way to scale well is to have bad single-core performance\" (Blind Freddie)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [coulomb] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Preparing vdw for lambda=0\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -277102597\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 2 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Raw data is like raw sewage, it requires some processing before it can be spread around. The opposite is true of theories.\" (Jim Carr)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.05\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1125393\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Millions saw the apple fall, Newton was the only one who asked why?\" (Bernard Baruch)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.1\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -283645253\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Millions saw the apple fall, Newton was the only one who asked why?\" (Bernard Baruch)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.2\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -33628482\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I never thought about breaking barriers, I was just interested in what I was doing and kept going.\" (Barbara Liskov)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.3\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 2130180031\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Jesus Not Only Saves, He Also Frequently Makes Backups.\" (Myron Bradshaw)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.4\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 2128084273\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Jesus Not Only Saves, He Also Frequently Makes Backups.\" (Myron Bradshaw)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1133076737\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.6\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1543503550\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.65\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1283854372\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I Was Born to Have Adventure\" (F. Zappa)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.7\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1613856850\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I Was Born to Have Adventure\" (F. Zappa)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -335680515\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The Microsecond is Within Reach\" (P.J. Van Maaren)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.8\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -811074625\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A protein is a chain of letters.\" (Julie Bernauer)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.85\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -206046313\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A protein is a chain of letters.\" (Julie Bernauer)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.9\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1214978\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"...sometimes a scream is better than a thesis.\" (Ralph Waldo Emerson)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.95\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1481185425\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"...sometimes a scream is better than a thesis.\" (Ralph Waldo Emerson)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -549716569\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Sisters Have Always Fascinated Me\" (Speech)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [vdw] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Saved state information to '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep'; reload later with G = Ghyd(filename='/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep').\n", + "mdpow.fep : INFO Finished setting up all individual simulations. Now run them...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -136445963\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top'],\n", + " 'maxwarn': 1,\n", + " 'couple-intramol': 'no',\n", + " 'couple_lambda0': 'vdw',\n", + " 'couple_lambda1': 'none',\n", + " 'sc_alpha': 0.5,\n", + " 'sc_power': 1,\n", + " 'sc_sigma': 0.3,\n", + " 'separate-dhdl-file': 'no',\n", + " 'ref_t': 300.0,\n", + " 'gen_temp': 300.0,\n", + " 'free_energy': 'yes',\n", + " 'couple_moltype': 'BENZ',\n", + " 'init_lambda_state': 15,\n", + " 'fep_lambdas': array([0. , 0.05, 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.65, 0.7 , 0.75,\n", + " 0.8 , 0.85, 0.9 , 0.95, 1. ]),\n", + " 'calc_lambda_neighbors': -1}" + ] + }, + "execution_count": 41, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import mdpow.fep\n", + "\n", + "gwat = mdpow.fep.Ghyd(simulation=sim, runtime=1e+3, mdp=str(RUN_FILE.absolute()))\n", + "gwat.setup(dt=0.02)\n", + "\n", + "# run multiple simulations on cluster" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "These could be run on a cluster using the `local.sh` scripts, but with Martini they can be done on a local machine in a reasonable amount of time (10-15 minutes on a desktop machine with a GTX 1080). " + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.025 0.006 396.8\n", + " (ns/day) (hour/ns)\n", + "Performance: 272.359 0.088\n", + "\n", + "GROMACS reminds you: \"I Caught It In the Face\" (P.J. Harvey)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.261\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 13 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.049 0.012 398.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 139.630 0.172\n", + "\n", + "GROMACS reminds you: \"I Caught It In the Face\" (P.J. Harvey)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 15 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.168 0.042 398.1\n", + " (ns/day) (hour/ns)\n", + "Performance: 40.992 0.585\n", + "\n", + "GROMACS reminds you: \"I was a bit of an artist, and somewhere along the way had gotten the idea that computers could be used for animation and artists, because in-betweening was so tedious... Of course, everyone thought I was nuts.\" (Carla Meninsky, Atari engineer)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 20 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.031 0.008 397.9\n", + " (ns/day) (hour/ns)\n", + "Performance: 218.840 0.110\n", + "\n", + "GROMACS reminds you: \"Here's the Way It Might End\" (G. Michael)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.025 0.006 397.2\n", + " (ns/day) (hour/ns)\n", + "Performance: 275.308 0.087\n", + "\n", + "GROMACS reminds you: \"Christianity may be OK between consenting adults in private but should not be taught to young children.\" (Francis Crick)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.031 0.008 397.4\n", + " (ns/day) (hour/ns)\n", + "Performance: 224.333 0.107\n", + "\n", + "GROMACS reminds you: \"Move about like a Scientist, lay down, get kissed\" (Red Hot Chili Peppars)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.261\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 26 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.035 0.009 397.9\n", + " (ns/day) (hour/ns)\n", + "Performance: 195.832 0.123\n", + "\n", + "GROMACS reminds you: \"Move about like a Scientist, lay down, get kissed\" (Red Hot Chili Peppars)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.047 0.012 398.2\n", + " (ns/day) (hour/ns)\n", + "Performance: 146.089 0.164\n", + "\n", + "GROMACS reminds you: \"Restraint! What possible restraint?\" (Joseph Conrad)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.030 0.008 397.4\n", + " (ns/day) (hour/ns)\n", + "Performance: 225.401 0.106\n", + "\n", + "GROMACS reminds you: \"I'm a Jerk\" (F. Black)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 15 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.029 0.007 397.2\n", + " (ns/day) (hour/ns)\n", + "Performance: 237.803 0.101\n", + "\n", + "GROMACS reminds you: \"Two chemists walk into a bar. The first one says, 'I'll have some H2O.'. The second one says, 'I'll have some H2O, too'. He dies.\" (Anonymous)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 24 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.056 0.014 398.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 121.934 0.197\n", + "\n", + "GROMACS reminds you: \"Two chemists walk into a bar. The first one says, 'I'll have some H2O.'. The second one says, 'I'll have some H2O, too'. He dies.\" (Anonymous)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 30 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.047 0.012 398.3\n", + " (ns/day) (hour/ns)\n", + "Performance: 145.534 0.165\n", + "\n", + "GROMACS reminds you: \"Shake Yourself\" (YES)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 12 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.024 0.006 396.8\n", + " (ns/day) (hour/ns)\n", + "Performance: 291.637 0.082\n", + "\n", + "GROMACS reminds you: \"I think everybody should like everybody.\" (Andy Warhol)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 26 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.044 0.011 398.4\n", + " (ns/day) (hour/ns)\n", + "Performance: 155.175 0.155\n", + "\n", + "GROMACS reminds you: \"Shit Happens\" (Pulp Fiction)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.034 0.009 397.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 203.183 0.118\n", + "\n", + "GROMACS reminds you: \"A curious aspect of the theory of evolution is that everybody thinks he understands it.\" (Jacques Monod)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 17 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.023 0.006 396.7\n", + " (ns/day) (hour/ns)\n", + "Performance: 303.368 0.079\n", + "\n", + "GROMACS reminds you: \"If it weren't for bad luck, we'd have no luck at all\" (The Unthanks)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 36 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.045 0.011 398.3\n", + " (ns/day) (hour/ns)\n", + "Performance: 152.222 0.158\n", + "\n", + "GROMACS reminds you: \"If it weren't for bad luck, we'd have no luck at all\" (The Unthanks)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 11 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.029 0.007 397.4\n", + " (ns/day) (hour/ns)\n", + "Performance: 233.731 0.103\n", + "\n", + "GROMACS reminds you: \"Move Over Hogey Bear\" (Urban Dance Squad)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 12 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.029 0.007 397.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 233.889 0.103\n", + "\n", + "GROMACS reminds you: \"Scientists do not join hands every Sunday and sing \"Yes gravity is real! I know gravity is real! I will have faith! I believe in my heart that what goes up, up, up must come down, down, down. Amen!\" If they did, we would think they were pretty insecure about the concept.\" (Dan Barker)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 15 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.024 0.006 396.9\n", + " (ns/day) (hour/ns)\n", + "Performance: 283.481 0.085\n", + "\n", + "GROMACS reminds you: \"Scientists do not join hands every Sunday and sing \"Yes gravity is real! I know gravity is real! I will have faith! I believe in my heart that what goes up, up, up must come down, down, down. Amen!\" If they did, we would think they were pretty insecure about the concept.\" (Dan Barker)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.028 0.007 397.4\n", + " (ns/day) (hour/ns)\n", + "Performance: 242.660 0.099\n", + "\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + } + ], + "source": [ + "for dir_ in gwat.fep_dirs():\n", + " r = gromacs.run.MDrunner(\n", + " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=True\n", + " )\n", + " r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Finally, we read the `.edr` files from the disk to get the energy reported by Gromacs and use `alchemlyb` to determine the free energy of solvation." + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [FEP/water] Converting EDR -> XVG.bz2\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/#md.xvg.1#\n", + "Reading energy frame 140 time 560.000 mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", + "\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/#md.xvg.1#\n", + "Reading energy frame 13 time 52.000 " + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/#md.xvg.1#\n", + "Reading energy frame 200 time 800.000 mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/#md.xvg.1#\n", + "Reading energy frame 200 time 800.000 mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"set: No match.\" (tcsh)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"set: No match.\" (tcsh)\n", + "\n", + "mdpow.fep : INFO Analysis stride is 1.\n", + "mdpow.fep : INFO Analysis starts from frame 0.\n", + "mdpow.fep : INFO Analysis stops at frame None.\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg' with bzip2\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Finding dgdl xvg files, reading with stride=1 permissive=False.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0000\n", + "\u001b[32m2023-09-04 22:40:31.863\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:31.865\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.78.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:31.866\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.9740.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0250\n", + "\u001b[32m2023-09-04 22:40:31.949\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:31.951\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 20.06.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:31.952\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 238.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 10.4664.\n", + "mdpow.fep : INFO The data are subsampled every 11 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0500\n", + "\u001b[32m2023-09-04 22:40:32.022\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.028\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 43.47.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.030\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 114.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 21.8509.\n", + "mdpow.fep : INFO The data are subsampled every 22 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0750\n", + "\u001b[32m2023-09-04 22:40:32.108\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.109\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 23.00.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.111\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 208.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.9760.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 1000\n", + "\u001b[32m2023-09-04 22:40:32.180\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.182\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 33.72.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.184\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 147.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 16.9456.\n", + "mdpow.fep : INFO The data are subsampled every 17 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0000\n", + "\u001b[32m2023-09-04 22:40:32.400\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.402\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 34.54.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.403\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 143.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 17.4196.\n", + "mdpow.fep : INFO The data are subsampled every 18 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0050\n", + "\u001b[32m2023-09-04 22:40:32.612\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.615\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 20.10.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.616\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 238.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 10.4664.\n", + "mdpow.fep : INFO The data are subsampled every 11 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0100\n", + "\u001b[32m2023-09-04 22:40:32.824\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.825\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.47.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.826\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.4793.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0200\n", + "\u001b[32m2023-09-04 22:40:33.054\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.056\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 27.85.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.057\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 178.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 13.9944.\n", + "mdpow.fep : INFO The data are subsampled every 14 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0300\n", + "\u001b[32m2023-09-04 22:40:33.298\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.300\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 27.51.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.302\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 178.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 13.9944.\n", + "mdpow.fep : INFO The data are subsampled every 14 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0400\n", + "\u001b[32m2023-09-04 22:40:33.555\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.557\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.25.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.558\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.9740.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0500\n", + "\u001b[32m2023-09-04 22:40:33.818\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.820\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 24.63.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.820\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 200.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.4550.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0600\n", + "\u001b[32m2023-09-04 22:40:34.042\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.047\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 42.95.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.048\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 116.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 21.4741.\n", + "mdpow.fep : INFO The data are subsampled every 22 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0650\n", + "\u001b[32m2023-09-04 22:40:34.274\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.276\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.73.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.277\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.4793.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0700\n", + "\u001b[32m2023-09-04 22:40:34.611\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.616\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.96.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.617\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.4793.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0750\n", + "\u001b[32m2023-09-04 22:40:34.863\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.865\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.68.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.866\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.9740.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0800\n", + "\u001b[32m2023-09-04 22:40:35.091\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.094\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 32.94.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.095\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 151.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 16.4967.\n", + "mdpow.fep : INFO The data are subsampled every 17 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0850\n", + "\u001b[32m2023-09-04 22:40:35.343\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.349\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 40.21.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.350\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 122.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 20.4180.\n", + "mdpow.fep : INFO The data are subsampled every 21 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0900\n", + "\u001b[32m2023-09-04 22:40:35.564\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.567\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 29.12.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.568\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 167.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 14.9162.\n", + "mdpow.fep : INFO The data are subsampled every 15 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0950\n", + "\u001b[32m2023-09-04 22:40:35.787\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.788\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.51.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.789\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 1000\n", + "\u001b[32m2023-09-04 22:40:35.996\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.998\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.19.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.999\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.4793.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", + "mdpow.fep : INFO DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (coulomb) 1.10771e-15 (0.00) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (vdw) -6.74471 (0.27) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (Gibbs) 6.74471 (0.27) kJ/mol\n" + ] + }, + { + "data": { + "text/plain": [ + "6.74471 (0.269555)" + ] + }, + "execution_count": 43, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "gwat.convert_edr()\n", + "gwat.analyze_alchemlyb()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Octanol solvation\n", + "\n", + "Now, we repeat the exact same steps as above but using an `OctanolSimulation`." + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/octanol.gro'...\n", + " :-) GROMACS - gmx editconf, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 4.0\n", + "\n", + "\n", + "Back Off! I just backed up boxed.gro to ./#boxed.gro.1#\n", + "\n", + "GROMACS reminds you: \"Sir, spare your threats: The bug which you would fright me with I seek.\" (Hermione, Act III, scene II of Shakespeare's Winter's Tale)\n", + "\n", + " :-) GROMACS - gmx solvate, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx solvate -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -cp boxed.gro -cs /home/awsm/MDPOW/doc/examples/martini/octanol.gro -o solvated.gro\n", + "\n", + "Reading solute configuration\n", + "Reading solvent configuration\n", + "\n", + "Initialising inter-atomic distances...\n", + "Generating solvent configuration\n", + "Will generate new solvent configuration of 2x2x2 boxes\n", + "Solvent box contains 5943 atoms in 1981 residues\n", + "Removed 828 solvent atoms due to solvent-solvent overlap\n", + "Removed 3 solvent atoms due to solute-solvent overlap\n", + "Sorting configuration\n", + "Found 1 molecule type:\n", + " OCO ( 3 atoms): 1704 residues\n", + "Generated solvent containing 5112 atoms in 1704 residues\n", + "Writing generated configuration to solvated.gro\n", + "\n", + "Back Off! I just backed up solvated.gro to ./#solvated.gro.1#\n", + "\n", + "Output configuration contains 5115 atoms in 1705 residues\n", + "Volume : 399.981 (nm^3)\n", + "Density : 389.199 (g/l)\n", + "Number of solvent molecules: 1704 \n", + "\n", + "Processing topology\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#system.top.2#\n", + "\n", + "GROMACS reminds you: \"Sir, spare your threats: The bug which you would fright me with I seek.\" (Hermione, Act III, scene II of Shakespeare's Winter's Tale)\n", + "\n", + "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/octanol.gro\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note that major changes are planned in future for editconf, to improve usability and utility.\n", + "Read 3 atoms\n", + "Volume: 4050 nm^3, corresponds to roughly 1822500 electrons\n", + "No velocities found\n", + " system size : 0.210 0.160 0.248 (nm)\n", + " diameter : 0.270 (nm)\n", + " center : 2.987 0.606 2.315 (nm)\n", + " box vectors : 15.000 15.000 18.000 (nm)\n", + " box angles : 90.00 90.00 90.00 (degrees)\n", + " box volume :4050.00 (nm^3)\n", + " shift : 3.216 5.597 0.609 (nm)\n", + "new center : 6.203 6.203 2.924 (nm)\n", + "new box vectors : 8.270 8.270 8.270 (nm)\n", + "new box angles : 60.00 60.00 90.00 (degrees)\n", + "new box volume : 399.98 (nm^3)\n", + "\n", + "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", + " based on residue and atom names, since they could not be\n", + " definitively assigned from the information in your input\n", + " files. These guessed numbers might deviate from the mass\n", + " and radius of the atom type. Please check the output\n", + " files if necessary. Note, that this functionality may\n", + " be removed in a future GROMACS version. Please, consider\n", + " using another file format for your input.\n", + "\n", + "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n", + "from the source below. This means the results may be different\n", + "compared to previous GROMACS versions.\n", + "\n", + "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n", + "A. Bondi\n", + "van der Waals Volumes and Radii\n", + "J. Phys. Chem. 68 (1964) pp. 441-451\n", + "-------- -------- --- Thank You --- -------- --------\n", + "\n", + "Adding line for 1704 solvent molecules with resname (OCO) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] After solvation: total charge qtot = 0 = 0\n", + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO Building the main index file 'main.ndx'...\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.2#\n", + "\n", + "GROMACS reminds you: \"Sir, spare your threats: The bug which you would fright me with I seek.\" (Hermione, Act III, scene II of Shakespeare's Winter's Tale)\n", + "\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -n main.ndx -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.3#\n", + "\n", + "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n", + "\n", + " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx trjconv -ur compact -center -boxcenter tric -pbc mol -f ionized.gro -s ionized.tpr -o compact.pdb -n main.ndx\n", + "\n", + "Will write pdb: Protein data bank file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Group 0 ( System) has 5115 elements\n", + "Group 1 ( Other) has 5115 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( OCO) has 5112 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 5112 elements\n", + "Select a group: Group 0 ( System) has 5115 elements\n", + "Group 1 ( Other) has 5115 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( OCO) has 5112 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 5112 elements\n", + "Select a group: Reading frames from gro file 'This is an auto generated system', 5115 atoms.\n", + "Reading frame 0 time 0.000 \n", + "Precision of ionized.gro is 0.001 (nm)\n", + "\n", + "Back Off! I just backed up compact.pdb to ./#compact.pdb.1#\n", + "Last frame 0 time 0.000 \n", + " -> frame 0 time 0.000 \n", + "Last written: frame 0 time 0.000\n", + "\n", + "\n", + "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n", + "\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -f /tmp/tmpxe8vdy7l.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -nov\n", + "\n", + "\n", + "NOTE 1 [file /tmp/tmpxe8vdy7l.mdp]:\n", + " For a correct single-point energy evaluation with nsteps = 0, use\n", + " continuation = yes to avoid constraining the input coordinates.\n", + "\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#pp_system.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note that major changes are planned in future for trjconv, to improve usability and utility.\n", + "Select group for centering\n", + "Selected 4: '__main__'\n", + "Select group for output\n", + "Selected 0: 'System'\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + "NOTE 2 [file system.top, line 28]:\n", + " For energy conservation with LINCS, lincs_iter should be 2 or larger.\n", + "\n", + "\n", + "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "NOTE 3 [file /tmp/tmpxe8vdy7l.mdp]:\n", + " NVE simulation with an initial temperature of zero: will use a Verlet\n", + " buffer of 10%. Check your energy drift!\n", + "\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top', mdp='em.mdp' ...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'em.mdp': ['maxwarn', 'pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n", + "Command line:\n", + " gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -maxwarn 1 -pp processed.top\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -105579659\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "Analysing residue names:\n", + "There are: 1705 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 0 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "Back Off! I just backed up em.tpr to ./#em.tpr.1#\n", + "\n", + "GROMACS reminds you: \"You Can Always Go On Ricky Lake\" (Offspring)\n", + "\n", + "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/run.py:423: AutoCorrectionWarning: No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + " warnings.warn(wmsg, category=AutoCorrectionWarning)\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n", + "Command line:\n", + " gmx mdrun -v -stepout 10 -deffnm em -c em.pdb\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1459009023\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "Analysing residue names:\n", + "There are: 1705 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 1 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + "Back Off! I just backed up em.log to ./#em.log.1#\n", + "Reading file em.tpr, VERSION 2023.2 (single precision)\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "\n", + "Back Off! I just backed up em.trr to ./#em.trr.1#\n", + "\n", + "Back Off! I just backed up em.edr to ./#em.edr.1#\n", + "\n", + "Steepest Descents:\n", + " Tolerance (Fmax) = 1.00000e+01\n", + " Number of steps = 1000\n", + "Step= 0, Dmax= 1.0e-02 nm, Epot= 1.02801e+07 Fmax= 2.05315e+07, atom= 5083\n", + "Step= 1, Dmax= 1.0e-02 nm, Epot= 7.41994e+06 Fmax= 5.74654e+06, atom= 3110\n", + "Step= 2, Dmax= 1.2e-02 nm, Epot= 4.40326e+06 Fmax= 2.44532e+06, atom= 4997\n", + "Step= 3, Dmax= 1.4e-02 nm, Epot= 2.73795e+06 Fmax= 9.51879e+05, atom= 1685\n", + "Step= 4, Dmax= 1.7e-02 nm, Epot= 1.53428e+06 Fmax= 4.51665e+05, atom= 1684\n", + "Step= 5, Dmax= 2.1e-02 nm, Epot= 8.87445e+05 Fmax= 1.90248e+05, atom= 1990\n", + "Step= 6, Dmax= 2.5e-02 nm, Epot= 4.61156e+05 Fmax= 1.05731e+05, atom= 3691\n", + "Step= 7, Dmax= 3.0e-02 nm, Epot= 2.59013e+05 Fmax= 7.39295e+04, atom= 3626\n", + "Step= 8, Dmax= 3.6e-02 nm, Epot= 1.57144e+05 Fmax= 4.51091e+04, atom= 3691\n", + "Step= 9, Dmax= 4.3e-02 nm, Epot= 8.70638e+04 Fmax= 3.11807e+04, atom= 3047\n", + "Step= 10, Dmax= 5.2e-02 nm, Epot= 4.74060e+04 Fmax= 1.09883e+05, atom= 3020\n", + "Step= 11, Dmax= 6.2e-02 nm, Epot= 3.89493e+04 Fmax= 1.54250e+04, atom= 1088\n", + "Step= 12, Dmax= 7.4e-02 nm, Epot= 6.83725e+03 Fmax= 1.68745e+04, atom= 1088\n", + "Step= 13, Dmax= 8.9e-02 nm, Epot= -4.12860e+03 Fmax= 1.03436e+04, atom= 1088\n", + "Step= 14, Dmax= 1.1e-01 nm, Epot= -1.13031e+04 Fmax= 1.60202e+05, atom= 4\n", + "Step= 15, Dmax= 1.3e-01 nm, Epot= -1.48685e+04 Fmax= 1.22373e+04, atom= 4\n", + "Step= 16, Dmax= 1.5e-01 nm, Epot= -2.01121e+04 Fmax= 3.01368e+04, atom= 4\n", + "Step= 17, Dmax= 1.8e-01 nm, Epot= -2.17951e+04 Fmax= 4.10915e+04, atom= 2520\n", + "Step= 18, Dmax= 2.2e-01 nm, Epot= -2.41457e+04 Fmax= 2.58494e+04, atom= 4\n", + "Step= 19, Dmax= 2.7e-01 nm, Epot= -2.66241e+04 Fmax= 2.69426e+04, atom= 835\n", + "Step= 23, Dmax= 4.0e-02 nm, Epot= -2.72906e+04 Fmax= 1.12460e+04, atom= 5360\n", + "Step= 24, Dmax= 4.8e-02 nm, Epot= -2.82619e+04 Fmax= 8.89296e+03, atom= 3110\n", + "Step= 25, Dmax= 5.8e-02 nm, Epot= -2.94485e+04 Fmax= 7.02511e+03, atom= 835\n", + "Step= 26, Dmax= 6.9e-02 nm, Epot= -3.10719e+04 Fmax= 4.20729e+03, atom= 835\n", + "Step= 27, Dmax= 8.3e-02 nm, Epot= -3.33641e+04 Fmax= 1.18154e+04, atom= 835\n", + "Step= 28, Dmax= 9.9e-02 nm, Epot= -3.46020e+04 Fmax= 2.13219e+03, atom= 3110\n", + "Step= 29, Dmax= 1.2e-01 nm, Epot= -3.82089e+04 Fmax= 4.27789e+04, atom= 3110\n", + "Step= 30, Dmax= 1.4e-01 nm, Epot= -3.94414e+04 Fmax= 2.82683e+03, atom= 536\n", + "Step= 31, Dmax= 1.7e-01 nm, Epot= -3.96515e+04 Fmax= 1.23669e+05, atom= 413\n", + "Step= 33, Dmax= 1.0e-01 nm, Epot= -4.13623e+04 Fmax= 3.78120e+04, atom= 413\n", + "Step= 34, Dmax= 1.2e-01 nm, Epot= -4.20929e+04 Fmax= 3.45758e+03, atom= 5051\n", + "Step= 35, Dmax= 1.5e-01 nm, Epot= -4.35947e+04 Fmax= 9.20874e+03, atom= 5051\n", + "Step= 36, Dmax= 1.8e-01 nm, Epot= -4.39134e+04 Fmax= 4.39989e+03, atom= 413\n", + "Step= 37, Dmax= 2.1e-01 nm, Epot= -4.44859e+04 Fmax= 2.43471e+04, atom= 5050\n", + "Step= 39, Dmax= 1.3e-01 nm, Epot= -4.46805e+04 Fmax= 3.27215e+04, atom= 5113\n", + "Step= 40, Dmax= 1.5e-01 nm, Epot= -4.53859e+04 Fmax= 6.23654e+03, atom= 1883\n", + "Step= 42, Dmax= 9.2e-02 nm, Epot= -4.59237e+04 Fmax= 1.73940e+03, atom= 1883\n", + "Step= 43, Dmax= 1.1e-01 nm, Epot= -4.70801e+04 Fmax= 2.89875e+03, atom= 1883\n", + "Step= 44, Dmax= 1.3e-01 nm, Epot= -4.77589e+04 Fmax= 3.05609e+03, atom= 1360\n", + "Step= 45, Dmax= 1.6e-01 nm, Epot= -4.80474e+04 Fmax= 1.33101e+04, atom= 1360\n", + "Step= 46, Dmax= 1.9e-01 nm, Epot= -4.84228e+04 Fmax= 6.33088e+03, atom= 567\n", + "Step= 48, Dmax= 1.1e-01 nm, Epot= -4.88170e+04 Fmax= 1.25395e+03, atom= 1608\n", + "Step= 49, Dmax= 1.4e-01 nm, Epot= -4.97575e+04 Fmax= 4.33496e+03, atom= 693\n", + "Step= 50, Dmax= 1.7e-01 nm, Epot= -5.01312e+04 Fmax= 3.75784e+03, atom= 1338\n", + "Step= 52, Dmax= 9.9e-02 nm, Epot= -5.02226e+04 Fmax= 9.33880e+03, atom= 2954\n", + "Step= 54, Dmax= 6.0e-02 nm, Epot= -5.04442e+04 Fmax= 1.97341e+03, atom= 144\n", + "Step= 55, Dmax= 7.1e-02 nm, Epot= -5.07143e+04 Fmax= 1.32154e+03, atom= 144\n", + "Step= 56, Dmax= 8.6e-02 nm, Epot= -5.11246e+04 Fmax= 1.28381e+03, atom= 144\n", + "Step= 57, Dmax= 1.0e-01 nm, Epot= -5.15390e+04 Fmax= 2.41925e+03, atom= 144\n", + "Step= 58, Dmax= 1.2e-01 nm, Epot= -5.18157e+04 Fmax= 1.10336e+03, atom= 2954\n", + "Step= 60, Dmax= 7.4e-02 nm, Epot= -5.21376e+04 Fmax= 1.22571e+03, atom= 3046\n", + "Step= 62, Dmax= 4.4e-02 nm, Epot= -5.22802e+04 Fmax= 1.99710e+03, atom= 3046\n", + "Step= 63, Dmax= 5.3e-02 nm, Epot= -5.24430e+04 Fmax= 1.13368e+03, atom= 444\n", + "Step= 64, Dmax= 6.4e-02 nm, Epot= -5.26101e+04 Fmax= 2.51858e+03, atom= 444\n", + "Step= 65, Dmax= 7.7e-02 nm, Epot= -5.27376e+04 Fmax= 1.69816e+03, atom= 3046\n", + "Step= 66, Dmax= 9.2e-02 nm, Epot= -5.27505e+04 Fmax= 4.60827e+03, atom= 3046\n", + "Step= 67, Dmax= 1.1e-01 nm, Epot= -5.29464e+04 Fmax= 2.66046e+03, atom= 444\n", + "Step= 68, Dmax= 1.3e-01 nm, Epot= -5.30886e+04 Fmax= 3.10115e+03, atom= 1079\n", + "Step= 70, Dmax= 8.0e-02 nm, Epot= -5.32855e+04 Fmax= 8.36880e+02, atom= 1079\n", + "Step= 72, Dmax= 4.8e-02 nm, Epot= -5.34753e+04 Fmax= 1.52218e+03, atom= 2567\n", + "Step= 73, Dmax= 5.7e-02 nm, Epot= -5.35846e+04 Fmax= 9.08475e+02, atom= 3179\n", + "Step= 74, Dmax= 6.9e-02 nm, Epot= -5.37531e+04 Fmax= 3.31739e+03, atom= 2567\n", + "Step= 75, Dmax= 8.3e-02 nm, Epot= -5.38422e+04 Fmax= 8.90771e+02, atom= 3179\n", + "Step= 76, Dmax= 9.9e-02 nm, Epot= -5.39374e+04 Fmax= 7.71798e+03, atom= 2567\n", + "Step= 77, Dmax= 1.2e-01 nm, Epot= -5.41298e+04 Fmax= 1.05874e+03, atom= 2567\n", + "Step= 79, Dmax= 7.1e-02 nm, Epot= -5.43156e+04 Fmax= 5.14630e+02, atom= 4622\n", + "Step= 80, Dmax= 8.6e-02 nm, Epot= -5.43995e+04 Fmax= 1.02555e+04, atom= 4622\n", + "Step= 81, Dmax= 1.0e-01 nm, Epot= -5.46246e+04 Fmax= 1.13109e+03, atom= 3179\n", + "Step= 82, Dmax= 1.2e-01 nm, Epot= -5.48060e+04 Fmax= 1.37699e+03, atom= 2567\n", + "Step= 83, Dmax= 1.5e-01 nm, Epot= -5.48334e+04 Fmax= 2.05696e+03, atom= 2567\n", + "Step= 84, Dmax= 1.8e-01 nm, Epot= -5.49886e+04 Fmax= 2.14840e+03, atom= 2567\n", + "Step= 85, Dmax= 2.1e-01 nm, Epot= -5.50857e+04 Fmax= 2.05082e+03, atom= 2567\n", + "Step= 87, Dmax= 1.3e-01 nm, Epot= -5.52320e+04 Fmax= 9.84210e+02, atom= 2567\n", + "Step= 89, Dmax= 7.7e-02 nm, Epot= -5.54016e+04 Fmax= 7.76042e+02, atom= 4623\n", + "Step= 90, Dmax= 9.2e-02 nm, Epot= -5.54718e+04 Fmax= 2.97639e+03, atom= 3180\n", + "Step= 91, Dmax= 1.1e-01 nm, Epot= -5.55854e+04 Fmax= 7.51557e+02, atom= 3180\n", + "Step= 93, Dmax= 6.6e-02 nm, Epot= -5.57277e+04 Fmax= 5.56224e+02, atom= 2566\n", + "Step= 94, Dmax= 7.9e-02 nm, Epot= -5.58208e+04 Fmax= 8.09355e+02, atom= 3568\n", + "Step= 95, Dmax= 9.5e-02 nm, Epot= -5.58278e+04 Fmax= 3.70043e+03, atom= 3015\n", + "Step= 96, Dmax= 1.1e-01 nm, Epot= -5.59803e+04 Fmax= 7.92915e+02, atom= 3015\n", + "Step= 97, Dmax= 1.4e-01 nm, Epot= -5.60522e+04 Fmax= 1.74485e+03, atom= 3528\n", + "Step= 99, Dmax= 8.2e-02 nm, Epot= -5.61793e+04 Fmax= 1.30159e+03, atom= 3207\n", + "Step= 100, Dmax= 9.9e-02 nm, Epot= -5.62395e+04 Fmax= 1.73043e+03, atom= 3306\n", + "Step= 101, Dmax= 1.2e-01 nm, Epot= -5.63205e+04 Fmax= 3.38021e+02, atom= 2922\n", + "Step= 102, Dmax= 1.4e-01 nm, Epot= -5.63321e+04 Fmax= 3.14597e+03, atom= 3306\n", + "Step= 103, Dmax= 1.7e-01 nm, Epot= -5.66195e+04 Fmax= 9.63577e+02, atom= 3306\n", + "Step= 105, Dmax= 1.0e-01 nm, Epot= -5.66649e+04 Fmax= 2.46338e+03, atom= 3207\n", + "Step= 106, Dmax= 1.2e-01 nm, Epot= -5.66681e+04 Fmax= 2.93470e+03, atom= 3528\n", + "Step= 107, Dmax= 1.5e-01 nm, Epot= -5.67116e+04 Fmax= 9.98182e+02, atom= 3015\n", + "Step= 108, Dmax= 1.8e-01 nm, Epot= -5.67160e+04 Fmax= 4.01710e+03, atom= 3568\n", + "Step= 109, Dmax= 2.1e-01 nm, Epot= -5.67314e+04 Fmax= 2.60014e+03, atom= 4623\n", + "Step= 110, Dmax= 2.6e-01 nm, Epot= -5.68128e+04 Fmax= 1.55369e+03, atom= 4632\n", + "Step= 112, Dmax= 1.5e-01 nm, Epot= -5.69097e+04 Fmax= 9.06986e+02, atom= 4624\n", + "Step= 114, Dmax= 9.2e-02 nm, Epot= -5.70090e+04 Fmax= 5.23911e+02, atom= 4624\n", + "Step= 116, Dmax= 5.5e-02 nm, Epot= -5.70881e+04 Fmax= 4.07709e+02, atom= 4625\n", + "Step= 117, Dmax= 6.6e-02 nm, Epot= -5.71193e+04 Fmax= 7.37738e+02, atom= 4625\n", + "Step= 118, Dmax= 7.9e-02 nm, Epot= -5.71803e+04 Fmax= 7.59541e+02, atom= 4625\n", + "Step= 119, Dmax= 9.5e-02 nm, Epot= -5.72119e+04 Fmax= 8.99682e+02, atom= 4625\n", + "Step= 121, Dmax= 5.7e-02 nm, Epot= -5.73265e+04 Fmax= 2.51483e+02, atom= 2558\n", + "Step= 123, Dmax= 3.4e-02 nm, Epot= -5.73747e+04 Fmax= 4.44440e+02, atom= 2558\n", + "Step= 124, Dmax= 4.1e-02 nm, Epot= -5.74121e+04 Fmax= 3.55337e+02, atom= 4635\n", + "Step= 125, Dmax= 4.9e-02 nm, Epot= -5.74287e+04 Fmax= 1.20535e+03, atom= 285\n", + "Step= 126, Dmax= 5.9e-02 nm, Epot= -5.74910e+04 Fmax= 3.55226e+02, atom= 285\n", + "Step= 127, Dmax= 7.1e-02 nm, Epot= -5.75302e+04 Fmax= 1.48864e+03, atom= 285\n", + "Step= 128, Dmax= 8.5e-02 nm, Epot= -5.75701e+04 Fmax= 6.22858e+02, atom= 4635\n", + "Step= 130, Dmax= 5.1e-02 nm, Epot= -5.76114e+04 Fmax= 3.83218e+02, atom= 5043\n", + "Step= 131, Dmax= 6.1e-02 nm, Epot= -5.76603e+04 Fmax= 4.35957e+02, atom= 5043\n", + "Step= 133, Dmax= 3.7e-02 nm, Epot= -5.76969e+04 Fmax= 3.00286e+02, atom= 4635\n", + "Step= 134, Dmax= 4.4e-02 nm, Epot= -5.77359e+04 Fmax= 3.85366e+02, atom= 285\n", + "Step= 135, Dmax= 5.3e-02 nm, Epot= -5.77624e+04 Fmax= 7.50828e+02, atom= 285\n", + "Step= 136, Dmax= 6.4e-02 nm, Epot= -5.77981e+04 Fmax= 4.54376e+02, atom= 285\n", + "Step= 138, Dmax= 3.8e-02 nm, Epot= -5.78377e+04 Fmax= 1.40492e+02, atom= 5043\n", + "Step= 139, Dmax= 4.6e-02 nm, Epot= -5.78694e+04 Fmax= 7.93461e+02, atom= 4635\n", + "Step= 140, Dmax= 5.5e-02 nm, Epot= -5.79361e+04 Fmax= 6.63909e+02, atom= 285\n", + "Step= 141, Dmax= 6.6e-02 nm, Epot= -5.79552e+04 Fmax= 5.89226e+02, atom= 285\n", + "Step= 142, Dmax= 7.9e-02 nm, Epot= -5.79725e+04 Fmax= 9.40391e+02, atom= 285\n", + "Step= 143, Dmax= 9.5e-02 nm, Epot= -5.79907e+04 Fmax= 7.07770e+02, atom= 285\n", + "Step= 145, Dmax= 5.7e-02 nm, Epot= -5.80467e+04 Fmax= 2.48711e+02, atom= 5043\n", + "Step= 147, Dmax= 3.4e-02 nm, Epot= -5.80828e+04 Fmax= 1.80194e+02, atom= 4634\n", + "Step= 149, Dmax= 2.1e-02 nm, Epot= -5.81124e+04 Fmax= 1.76968e+02, atom= 4634\n", + "Step= 150, Dmax= 2.5e-02 nm, Epot= -5.81382e+04 Fmax= 2.74294e+02, atom= 2558\n", + "Step= 151, Dmax= 3.0e-02 nm, Epot= -5.81669e+04 Fmax= 2.65196e+02, atom= 2558\n", + "Step= 152, Dmax= 3.5e-02 nm, Epot= -5.81878e+04 Fmax= 3.79214e+02, atom= 2558\n", + "Step= 153, Dmax= 4.3e-02 nm, Epot= -5.82143e+04 Fmax= 3.92706e+02, atom= 2558\n", + "Step= 154, Dmax= 5.1e-02 nm, Epot= -5.82281e+04 Fmax= 5.24798e+02, atom= 2558\n", + "Step= 155, Dmax= 6.1e-02 nm, Epot= -5.82503e+04 Fmax= 5.79046e+02, atom= 2558\n", + "Step= 156, Dmax= 7.4e-02 nm, Epot= -5.82509e+04 Fmax= 7.28714e+02, atom= 2558\n", + "Step= 157, Dmax= 8.8e-02 nm, Epot= -5.82588e+04 Fmax= 8.45931e+02, atom= 2558\n", + "Step= 159, Dmax= 5.3e-02 nm, Epot= -5.83439e+04 Fmax= 2.05454e+02, atom= 2858\n", + "Step= 160, Dmax= 6.4e-02 nm, Epot= -5.83443e+04 Fmax= 1.29098e+03, atom= 285\n", + "Step= 161, Dmax= 7.6e-02 nm, Epot= -5.84063e+04 Fmax= 3.91486e+02, atom= 4635\n", + "Step= 163, Dmax= 4.6e-02 nm, Epot= -5.84326e+04 Fmax= 2.44490e+02, atom= 285\n", + "Step= 165, Dmax= 2.7e-02 nm, Epot= -5.84581e+04 Fmax= 2.18521e+02, atom= 2855\n", + "Step= 166, Dmax= 3.3e-02 nm, Epot= -5.84788e+04 Fmax= 2.95386e+02, atom= 285\n", + "Step= 167, Dmax= 4.0e-02 nm, Epot= -5.84927e+04 Fmax= 3.83630e+02, atom= 2558\n", + "Step= 168, Dmax= 4.7e-02 nm, Epot= -5.85106e+04 Fmax= 4.59339e+02, atom= 2558\n", + "Step= 169, Dmax= 5.7e-02 nm, Epot= -5.85206e+04 Fmax= 5.41944e+02, atom= 2558\n", + "Step= 170, Dmax= 6.8e-02 nm, Epot= -5.85312e+04 Fmax= 6.62982e+02, atom= 2558\n", + "Step= 172, Dmax= 4.1e-02 nm, Epot= -5.85911e+04 Fmax= 1.11736e+02, atom= 2858\n", + "Step= 173, Dmax= 4.9e-02 nm, Epot= -5.86252e+04 Fmax= 8.80132e+02, atom= 285\n", + "Step= 174, Dmax= 5.9e-02 nm, Epot= -5.86674e+04 Fmax= 2.93543e+02, atom= 285\n", + "Step= 176, Dmax= 3.5e-02 nm, Epot= -5.86879e+04 Fmax= 2.57437e+02, atom= 285\n", + "Step= 177, Dmax= 4.3e-02 nm, Epot= -5.86965e+04 Fmax= 4.14149e+02, atom= 285\n", + "Step= 178, Dmax= 5.1e-02 nm, Epot= -5.87122e+04 Fmax= 4.88773e+02, atom= 285\n", + "Step= 179, Dmax= 6.1e-02 nm, Epot= -5.87183e+04 Fmax= 5.02784e+02, atom= 285\n", + "Step= 181, Dmax= 3.7e-02 nm, Epot= -5.87685e+04 Fmax= 1.24716e+02, atom= 2558\n", + "Step= 182, Dmax= 4.4e-02 nm, Epot= -5.87783e+04 Fmax= 6.32760e+02, atom= 2558\n", + "Step= 183, Dmax= 5.3e-02 nm, Epot= -5.88269e+04 Fmax= 2.78799e+02, atom= 2558\n", + "Step= 185, Dmax= 3.2e-02 nm, Epot= -5.88438e+04 Fmax= 2.67023e+02, atom= 2558\n", + "Step= 186, Dmax= 3.8e-02 nm, Epot= -5.88562e+04 Fmax= 3.92228e+02, atom= 2558\n", + "Step= 187, Dmax= 4.6e-02 nm, Epot= -5.88719e+04 Fmax= 3.94399e+02, atom= 2558\n", + "Step= 188, Dmax= 5.5e-02 nm, Epot= -5.88777e+04 Fmax= 5.51790e+02, atom= 2558\n", + "Step= 189, Dmax= 6.6e-02 nm, Epot= -5.88898e+04 Fmax= 5.74763e+02, atom= 2558\n", + "Step= 191, Dmax= 3.9e-02 nm, Epot= -5.89313e+04 Fmax= 9.24066e+01, atom= 2558\n", + "Step= 192, Dmax= 4.7e-02 nm, Epot= -5.89464e+04 Fmax= 7.09055e+02, atom= 2558\n", + "Step= 193, Dmax= 5.7e-02 nm, Epot= -5.89983e+04 Fmax= 2.72586e+02, atom= 2558\n", + "Step= 195, Dmax= 3.4e-02 nm, Epot= -5.90113e+04 Fmax= 3.12088e+02, atom= 2558\n", + "Step= 196, Dmax= 4.1e-02 nm, Epot= -5.90177e+04 Fmax= 3.89366e+02, atom= 2558\n", + "Step= 197, Dmax= 4.9e-02 nm, Epot= -5.90259e+04 Fmax= 4.71057e+02, atom= 2750\n", + "Step= 199, Dmax= 2.9e-02 nm, Epot= -5.90633e+04 Fmax= 1.07989e+02, atom= 2750\n", + "Step= 200, Dmax= 3.5e-02 nm, Epot= -5.90842e+04 Fmax= 6.97884e+02, atom= 2750\n", + "Step= 201, Dmax= 4.2e-02 nm, Epot= -5.91077e+04 Fmax= 1.90523e+02, atom= 2750\n", + "Step= 203, Dmax= 2.5e-02 nm, Epot= -5.91226e+04 Fmax= 2.20171e+02, atom= 2750\n", + "Step= 204, Dmax= 3.1e-02 nm, Epot= -5.91348e+04 Fmax= 2.94176e+02, atom= 2750\n", + "Step= 205, Dmax= 3.7e-02 nm, Epot= -5.91476e+04 Fmax= 3.56281e+02, atom= 2750\n", + "Step= 206, Dmax= 4.4e-02 nm, Epot= -5.91563e+04 Fmax= 3.82359e+02, atom= 2750\n", + "Step= 207, Dmax= 5.3e-02 nm, Epot= -5.91628e+04 Fmax= 5.88973e+02, atom= 2750\n", + "Step= 208, Dmax= 6.3e-02 nm, Epot= -5.91732e+04 Fmax= 4.85093e+02, atom= 2750\n", + "Step= 210, Dmax= 3.8e-02 nm, Epot= -5.92039e+04 Fmax= 1.35743e+02, atom= 1037\n", + "Step= 211, Dmax= 4.6e-02 nm, Epot= -5.92141e+04 Fmax= 5.65706e+02, atom= 1037\n", + "Step= 212, Dmax= 5.5e-02 nm, Epot= -5.92410e+04 Fmax= 4.54354e+02, atom= 1037\n", + "Step= 214, Dmax= 3.3e-02 nm, Epot= -5.92579e+04 Fmax= 1.66848e+02, atom= 2750\n", + "Step= 215, Dmax= 3.9e-02 nm, Epot= -5.92647e+04 Fmax= 6.44873e+02, atom= 2750\n", + "Step= 216, Dmax= 4.7e-02 nm, Epot= -5.92871e+04 Fmax= 2.43525e+02, atom= 2750\n", + "Step= 218, Dmax= 2.8e-02 nm, Epot= -5.93006e+04 Fmax= 1.95952e+02, atom= 2750\n", + "Step= 219, Dmax= 3.4e-02 nm, Epot= -5.93089e+04 Fmax= 3.67029e+02, atom= 2750\n", + "Step= 220, Dmax= 4.1e-02 nm, Epot= -5.93240e+04 Fmax= 3.34144e+02, atom= 2750\n", + "Step= 221, Dmax= 4.9e-02 nm, Epot= -5.93247e+04 Fmax= 4.66065e+02, atom= 1037\n", + "Step= 222, Dmax= 5.9e-02 nm, Epot= -5.93346e+04 Fmax= 5.60595e+02, atom= 1037\n", + "Step= 224, Dmax= 3.5e-02 nm, Epot= -5.93648e+04 Fmax= 1.09633e+02, atom= 2750\n", + "Step= 225, Dmax= 4.2e-02 nm, Epot= -5.93780e+04 Fmax= 8.31451e+02, atom= 2750\n", + "Step= 226, Dmax= 5.1e-02 nm, Epot= -5.94053e+04 Fmax= 2.09115e+02, atom= 2750\n", + "Step= 228, Dmax= 3.1e-02 nm, Epot= -5.94176e+04 Fmax= 2.62302e+02, atom= 2750\n", + "Step= 229, Dmax= 3.7e-02 nm, Epot= -5.94262e+04 Fmax= 3.36118e+02, atom= 2750\n", + "Step= 230, Dmax= 4.4e-02 nm, Epot= -5.94357e+04 Fmax= 4.10895e+02, atom= 2750\n", + "Step= 231, Dmax= 5.3e-02 nm, Epot= -5.94403e+04 Fmax= 4.45711e+02, atom= 2750\n", + "Step= 233, Dmax= 3.2e-02 nm, Epot= -5.94655e+04 Fmax= 7.20466e+01, atom= 1037\n", + "Step= 234, Dmax= 3.8e-02 nm, Epot= -5.94950e+04 Fmax= 4.87951e+02, atom= 1037\n", + "Step= 235, Dmax= 4.6e-02 nm, Epot= -5.95155e+04 Fmax= 3.33452e+02, atom= 1037\n", + "Step= 237, Dmax= 2.7e-02 nm, Epot= -5.95271e+04 Fmax= 1.38156e+02, atom= 2750\n", + "Step= 238, Dmax= 3.3e-02 nm, Epot= -5.95330e+04 Fmax= 5.13054e+02, atom= 2750\n", + "Step= 239, Dmax= 3.9e-02 nm, Epot= -5.95524e+04 Fmax= 2.04268e+02, atom= 2750\n", + "Step= 241, Dmax= 2.4e-02 nm, Epot= -5.95633e+04 Fmax= 1.66953e+02, atom= 2750\n", + "Step= 242, Dmax= 2.8e-02 nm, Epot= -5.95715e+04 Fmax= 2.97517e+02, atom= 2750\n", + "Step= 243, Dmax= 3.4e-02 nm, Epot= -5.95832e+04 Fmax= 2.83477e+02, atom= 1037\n", + "Step= 244, Dmax= 4.1e-02 nm, Epot= -5.95869e+04 Fmax= 3.94152e+02, atom= 1037\n", + "Step= 245, Dmax= 4.9e-02 nm, Epot= -5.95965e+04 Fmax= 4.43375e+02, atom= 1037\n", + "Step= 247, Dmax= 2.9e-02 nm, Epot= -5.96171e+04 Fmax= 8.59002e+01, atom= 2750\n", + "Step= 248, Dmax= 3.5e-02 nm, Epot= -5.96313e+04 Fmax= 6.37273e+02, atom= 2750\n", + "Step= 249, Dmax= 4.2e-02 nm, Epot= -5.96541e+04 Fmax= 1.76496e+02, atom= 2750\n", + "Step= 251, Dmax= 2.5e-02 nm, Epot= -5.96643e+04 Fmax= 2.22371e+02, atom= 2750\n", + "Step= 252, Dmax= 3.0e-02 nm, Epot= -5.96723e+04 Fmax= 2.74291e+02, atom= 2750\n", + "Step= 253, Dmax= 3.7e-02 nm, Epot= -5.96804e+04 Fmax= 3.39338e+02, atom= 2750\n", + "Step= 254, Dmax= 4.4e-02 nm, Epot= -5.96857e+04 Fmax= 3.71865e+02, atom= 2750\n", + "Step= 255, Dmax= 5.3e-02 nm, Epot= -5.96876e+04 Fmax= 5.34522e+02, atom= 2750\n", + "Step= 256, Dmax= 6.3e-02 nm, Epot= -5.96929e+04 Fmax= 4.90829e+02, atom= 2750\n", + "Step= 258, Dmax= 3.8e-02 nm, Epot= -5.97230e+04 Fmax= 1.29100e+02, atom= 1037\n", + "Step= 259, Dmax= 4.5e-02 nm, Epot= -5.97247e+04 Fmax= 5.78329e+02, atom= 1037\n", + "Step= 260, Dmax= 5.5e-02 nm, Epot= -5.97496e+04 Fmax= 3.53992e+02, atom= 1037\n", + "Step= 262, Dmax= 3.3e-02 nm, Epot= -5.97610e+04 Fmax= 1.91255e+02, atom= 1037\n", + "Step= 264, Dmax= 2.0e-02 nm, Epot= -5.97701e+04 Fmax= 1.35681e+02, atom= 1037\n", + "Step= 265, Dmax= 2.4e-02 nm, Epot= -5.97786e+04 Fmax= 2.54210e+02, atom= 1037\n", + "Step= 266, Dmax= 2.8e-02 nm, Epot= -5.97881e+04 Fmax= 2.22014e+02, atom= 1037\n", + "Step= 267, Dmax= 3.4e-02 nm, Epot= -5.97931e+04 Fmax= 3.36883e+02, atom= 1037\n", + "Step= 268, Dmax= 4.1e-02 nm, Epot= -5.98018e+04 Fmax= 3.49815e+02, atom= 1037\n", + "Step= 269, Dmax= 4.9e-02 nm, Epot= -5.98032e+04 Fmax= 4.53508e+02, atom= 1037\n", + "Step= 270, Dmax= 5.9e-02 nm, Epot= -5.98085e+04 Fmax= 5.35072e+02, atom= 1037\n", + "Step= 272, Dmax= 3.5e-02 nm, Epot= -5.98330e+04 Fmax= 8.22722e+01, atom= 2750\n", + "Step= 273, Dmax= 4.2e-02 nm, Epot= -5.98371e+04 Fmax= 8.31920e+02, atom= 2750\n", + "Step= 274, Dmax= 5.1e-02 nm, Epot= -5.98695e+04 Fmax= 1.78990e+02, atom= 2750\n", + "Step= 276, Dmax= 3.0e-02 nm, Epot= -5.98776e+04 Fmax= 2.87462e+02, atom= 2750\n", + "Step= 277, Dmax= 3.6e-02 nm, Epot= -5.98843e+04 Fmax= 3.00568e+02, atom= 2750\n", + "Step= 278, Dmax= 4.4e-02 nm, Epot= -5.98884e+04 Fmax= 4.18449e+02, atom= 2750\n", + "Step= 279, Dmax= 5.3e-02 nm, Epot= -5.98928e+04 Fmax= 4.22419e+02, atom= 2750\n", + "Step= 281, Dmax= 3.2e-02 nm, Epot= -5.99127e+04 Fmax= 8.00841e+01, atom= 1037\n", + "Step= 282, Dmax= 3.8e-02 nm, Epot= -5.99217e+04 Fmax= 5.07395e+02, atom= 1037\n", + "Step= 283, Dmax= 4.5e-02 nm, Epot= -5.99439e+04 Fmax= 2.62831e+02, atom= 1037\n", + "Step= 285, Dmax= 2.7e-02 nm, Epot= -5.99519e+04 Fmax= 1.83905e+02, atom= 1037\n", + "Step= 286, Dmax= 3.3e-02 nm, Epot= -5.99549e+04 Fmax= 3.78590e+02, atom= 1037\n", + "Step= 287, Dmax= 3.9e-02 nm, Epot= -5.99652e+04 Fmax= 2.74147e+02, atom= 1037\n", + "Step= 289, Dmax= 2.4e-02 nm, Epot= -5.99761e+04 Fmax= 1.13455e+02, atom= 1037\n", + "Step= 290, Dmax= 2.8e-02 nm, Epot= -5.99826e+04 Fmax= 3.45366e+02, atom= 1037\n", + "Step= 291, Dmax= 3.4e-02 nm, Epot= -5.99945e+04 Fmax= 2.19360e+02, atom= 1037\n", + "Step= 293, Dmax= 2.0e-02 nm, Epot= -6.00023e+04 Fmax= 1.17656e+02, atom= 1037\n", + "Step= 294, Dmax= 2.4e-02 nm, Epot= -6.00091e+04 Fmax= 3.00515e+02, atom= 1037\n", + "Step= 295, Dmax= 2.9e-02 nm, Epot= -6.00184e+04 Fmax= 1.87183e+02, atom= 1037\n", + "Step= 296, Dmax= 3.5e-02 nm, Epot= -6.00195e+04 Fmax= 4.17089e+02, atom= 1037\n", + "Step= 297, Dmax= 4.2e-02 nm, Epot= -6.00310e+04 Fmax= 2.84840e+02, atom= 1037\n", + "Step= 299, Dmax= 2.5e-02 nm, Epot= -6.00418e+04 Fmax= 1.31955e+02, atom= 1037\n", + "Step= 300, Dmax= 3.0e-02 nm, Epot= -6.00463e+04 Fmax= 3.60137e+02, atom= 1037\n", + "Step= 301, Dmax= 3.6e-02 nm, Epot= -6.00579e+04 Fmax= 2.45266e+02, atom= 1037\n", + "Step= 303, Dmax= 2.2e-02 nm, Epot= -6.00661e+04 Fmax= 1.16807e+02, atom= 1037\n", + "Step= 304, Dmax= 2.6e-02 nm, Epot= -6.00720e+04 Fmax= 3.33042e+02, atom= 1037\n", + "Step= 305, Dmax= 3.1e-02 nm, Epot= -6.00822e+04 Fmax= 1.91207e+02, atom= 1037\n", + "Step= 307, Dmax= 1.9e-02 nm, Epot= -6.00896e+04 Fmax= 1.22868e+02, atom= 1037\n", + "Step= 308, Dmax= 2.3e-02 nm, Epot= -6.00962e+04 Fmax= 2.45731e+02, atom= 1037\n", + "Step= 309, Dmax= 2.7e-02 nm, Epot= -6.01039e+04 Fmax= 2.08716e+02, atom= 1037\n", + "Step= 310, Dmax= 3.3e-02 nm, Epot= -6.01076e+04 Fmax= 3.23587e+02, atom= 1037\n", + "Step= 311, Dmax= 3.9e-02 nm, Epot= -6.01146e+04 Fmax= 3.30965e+02, atom= 1037\n", + "Step= 312, Dmax= 4.7e-02 nm, Epot= -6.01152e+04 Fmax= 4.35908e+02, atom= 1037\n", + "Step= 313, Dmax= 5.6e-02 nm, Epot= -6.01193e+04 Fmax= 5.06340e+02, atom= 1037\n", + "Step= 315, Dmax= 3.4e-02 nm, Epot= -6.01402e+04 Fmax= 6.74224e+01, atom= 2750\n", + "Step= 317, Dmax= 2.0e-02 nm, Epot= -6.01506e+04 Fmax= 2.75903e+02, atom= 1037\n", + "Step= 318, Dmax= 2.4e-02 nm, Epot= -6.01599e+04 Fmax= 1.34990e+02, atom= 1037\n", + "Step= 319, Dmax= 2.9e-02 nm, Epot= -6.01621e+04 Fmax= 3.70568e+02, atom= 1037\n", + "Step= 320, Dmax= 3.5e-02 nm, Epot= -6.01737e+04 Fmax= 2.16357e+02, atom= 1037\n", + "Step= 322, Dmax= 2.1e-02 nm, Epot= -6.01817e+04 Fmax= 1.31919e+02, atom= 1037\n", + "Step= 323, Dmax= 2.5e-02 nm, Epot= -6.01867e+04 Fmax= 2.79645e+02, atom= 1037\n", + "Step= 324, Dmax= 3.0e-02 nm, Epot= -6.01951e+04 Fmax= 2.25485e+02, atom= 1037\n", + "Step= 325, Dmax= 3.6e-02 nm, Epot= -6.01964e+04 Fmax= 3.67171e+02, atom= 1037\n", + "Step= 326, Dmax= 4.4e-02 nm, Epot= -6.02041e+04 Fmax= 3.60232e+02, atom= 1037\n", + "Step= 328, Dmax= 2.6e-02 nm, Epot= -6.02166e+04 Fmax= 7.92455e+01, atom= 1037\n", + "Step= 329, Dmax= 3.1e-02 nm, Epot= -6.02207e+04 Fmax= 4.79290e+02, atom= 1037\n", + "Step= 330, Dmax= 3.8e-02 nm, Epot= -6.02388e+04 Fmax= 1.65514e+02, atom= 1037\n", + "Step= 332, Dmax= 2.3e-02 nm, Epot= -6.02444e+04 Fmax= 2.13497e+02, atom= 1037\n", + "Step= 333, Dmax= 2.7e-02 nm, Epot= -6.02497e+04 Fmax= 2.34472e+02, atom= 1037\n", + "Step= 334, Dmax= 3.3e-02 nm, Epot= -6.02538e+04 Fmax= 3.14438e+02, atom= 1037\n", + "Step= 335, Dmax= 3.9e-02 nm, Epot= -6.02584e+04 Fmax= 3.29824e+02, atom= 1037\n", + "Step= 336, Dmax= 4.7e-02 nm, Epot= -6.02588e+04 Fmax= 4.61035e+02, atom= 1037\n", + "Step= 337, Dmax= 5.6e-02 nm, Epot= -6.02622e+04 Fmax= 4.64117e+02, atom= 1037\n", + "Step= 339, Dmax= 3.4e-02 nm, Epot= -6.02836e+04 Fmax= 8.26266e+01, atom= 1037\n", + "Step= 340, Dmax= 4.1e-02 nm, Epot= -6.02865e+04 Fmax= 5.54988e+02, atom= 1037\n", + "Step= 341, Dmax= 4.9e-02 nm, Epot= -6.03081e+04 Fmax= 2.47292e+02, atom= 1037\n", + "Step= 343, Dmax= 2.9e-02 nm, Epot= -6.03138e+04 Fmax= 2.30271e+02, atom= 1037\n", + "Step= 344, Dmax= 3.5e-02 nm, Epot= -6.03161e+04 Fmax= 3.58030e+02, atom= 1037\n", + "Step= 345, Dmax= 4.2e-02 nm, Epot= -6.03217e+04 Fmax= 3.34048e+02, atom= 1037\n", + "Step= 347, Dmax= 2.5e-02 nm, Epot= -6.03334e+04 Fmax= 7.76801e+01, atom= 1037\n", + "Step= 348, Dmax= 3.0e-02 nm, Epot= -6.03398e+04 Fmax= 4.07179e+02, atom= 1037\n", + "Step= 349, Dmax= 3.6e-02 nm, Epot= -6.03535e+04 Fmax= 1.90604e+02, atom= 1037\n", + "Step= 351, Dmax= 2.2e-02 nm, Epot= -6.03590e+04 Fmax= 1.67562e+02, atom= 1037\n", + "Step= 352, Dmax= 2.6e-02 nm, Epot= -6.03628e+04 Fmax= 2.72241e+02, atom= 1037\n", + "Step= 353, Dmax= 3.1e-02 nm, Epot= -6.03686e+04 Fmax= 2.45528e+02, atom= 1037\n", + "Step= 354, Dmax= 3.8e-02 nm, Epot= -6.03690e+04 Fmax= 3.89593e+02, atom= 1037\n", + "Step= 355, Dmax= 4.5e-02 nm, Epot= -6.03747e+04 Fmax= 3.56036e+02, atom= 1037\n", + "Step= 357, Dmax= 2.7e-02 nm, Epot= -6.03881e+04 Fmax= 8.61068e+01, atom= 1037\n", + "Step= 358, Dmax= 3.3e-02 nm, Epot= -6.03886e+04 Fmax= 4.35313e+02, atom= 1037\n", + "Step= 359, Dmax= 3.9e-02 nm, Epot= -6.04053e+04 Fmax= 2.07639e+02, atom= 1037\n", + "Step= 361, Dmax= 2.3e-02 nm, Epot= -6.04109e+04 Fmax= 1.78364e+02, atom= 1037\n", + "Step= 362, Dmax= 2.8e-02 nm, Epot= -6.04121e+04 Fmax= 2.95268e+02, atom= 1037\n", + "Step= 363, Dmax= 3.4e-02 nm, Epot= -6.04179e+04 Fmax= 2.62369e+02, atom= 1037\n", + "Step= 365, Dmax= 2.0e-02 nm, Epot= -6.04286e+04 Fmax= 7.02098e+01, atom= 1037\n", + "Step= 367, Dmax= 1.2e-02 nm, Epot= -6.04340e+04 Fmax= 1.27299e+02, atom= 1037\n", + "Step= 368, Dmax= 1.5e-02 nm, Epot= -6.04391e+04 Fmax= 1.16376e+02, atom= 1037\n", + "Step= 369, Dmax= 1.7e-02 nm, Epot= -6.04420e+04 Fmax= 1.70247e+02, atom= 1037\n", + "Step= 370, Dmax= 2.1e-02 nm, Epot= -6.04457e+04 Fmax= 1.82795e+02, atom= 1949\n", + "Step= 372, Dmax= 1.3e-02 nm, Epot= -6.04557e+04 Fmax= 3.24653e+01, atom= 1223\n", + "Step= 373, Dmax= 1.5e-02 nm, Epot= -6.04636e+04 Fmax= 2.56892e+02, atom= 1223\n", + "Step= 374, Dmax= 1.8e-02 nm, Epot= -6.04776e+04 Fmax= 7.03043e+01, atom= 1223\n", + "Step= 376, Dmax= 1.1e-02 nm, Epot= -6.04828e+04 Fmax= 1.18501e+02, atom= 1223\n", + "Step= 377, Dmax= 1.3e-02 nm, Epot= -6.04876e+04 Fmax= 1.07331e+02, atom= 1223\n", + "Step= 378, Dmax= 1.6e-02 nm, Epot= -6.04915e+04 Fmax= 1.70629e+02, atom= 1223\n", + "Step= 379, Dmax= 1.9e-02 nm, Epot= -6.04965e+04 Fmax= 1.56634e+02, atom= 1223\n", + "Step= 380, Dmax= 2.3e-02 nm, Epot= -6.04986e+04 Fmax= 2.41043e+02, atom= 1223\n", + "Step= 381, Dmax= 2.7e-02 nm, Epot= -6.05037e+04 Fmax= 2.29850e+02, atom= 1223\n", + "Step= 383, Dmax= 1.6e-02 nm, Epot= -6.05126e+04 Fmax= 5.26314e+01, atom= 1223\n", + "Step= 384, Dmax= 1.9e-02 nm, Epot= -6.05193e+04 Fmax= 2.92343e+02, atom= 1223\n", + "Step= 385, Dmax= 2.3e-02 nm, Epot= -6.05295e+04 Fmax= 1.30780e+02, atom= 1223\n", + "Step= 387, Dmax= 1.4e-02 nm, Epot= -6.05342e+04 Fmax= 1.05053e+02, atom= 1223\n", + "Step= 388, Dmax= 1.7e-02 nm, Epot= -6.05381e+04 Fmax= 1.89563e+02, atom= 1223\n", + "Step= 389, Dmax= 2.0e-02 nm, Epot= -6.05433e+04 Fmax= 1.57603e+02, atom= 1223\n", + "Step= 390, Dmax= 2.4e-02 nm, Epot= -6.05448e+04 Fmax= 2.65033e+02, atom= 1223\n", + "Step= 391, Dmax= 2.9e-02 nm, Epot= -6.05503e+04 Fmax= 2.37203e+02, atom= 1223\n", + "Step= 393, Dmax= 1.7e-02 nm, Epot= -6.05586e+04 Fmax= 6.57889e+01, atom= 1223\n", + "Step= 394, Dmax= 2.1e-02 nm, Epot= -6.05627e+04 Fmax= 3.05352e+02, atom= 1223\n", + "Step= 395, Dmax= 2.5e-02 nm, Epot= -6.05727e+04 Fmax= 1.44005e+02, atom= 1223\n", + "Step= 397, Dmax= 1.5e-02 nm, Epot= -6.05773e+04 Fmax= 1.08536e+02, atom= 1223\n", + "Step= 398, Dmax= 1.8e-02 nm, Epot= -6.05807e+04 Fmax= 2.07503e+02, atom= 1223\n", + "Step= 399, Dmax= 2.2e-02 nm, Epot= -6.05861e+04 Fmax= 1.64592e+02, atom= 1223\n", + "Step= 400, Dmax= 2.6e-02 nm, Epot= -6.05864e+04 Fmax= 2.88908e+02, atom= 1223\n", + "Step= 401, Dmax= 3.1e-02 nm, Epot= -6.05924e+04 Fmax= 2.49418e+02, atom= 1223\n", + "Step= 403, Dmax= 1.9e-02 nm, Epot= -6.06012e+04 Fmax= 7.42693e+01, atom= 1223\n", + "Step= 404, Dmax= 2.3e-02 nm, Epot= -6.06030e+04 Fmax= 3.24604e+02, atom= 1223\n", + "Step= 405, Dmax= 2.7e-02 nm, Epot= -6.06140e+04 Fmax= 1.57066e+02, atom= 1223\n", + "Step= 407, Dmax= 1.6e-02 nm, Epot= -6.06188e+04 Fmax= 1.13301e+02, atom= 1223\n", + "Step= 408, Dmax= 1.9e-02 nm, Epot= -6.06213e+04 Fmax= 2.26259e+02, atom= 1223\n", + "Step= 409, Dmax= 2.3e-02 nm, Epot= -6.06271e+04 Fmax= 1.72987e+02, atom= 1223\n", + "Step= 411, Dmax= 1.4e-02 nm, Epot= -6.06328e+04 Fmax= 6.94849e+01, atom= 1223\n", + "Step= 412, Dmax= 1.7e-02 nm, Epot= -6.06371e+04 Fmax= 2.19846e+02, atom= 1223\n", + "Step= 413, Dmax= 2.0e-02 nm, Epot= -6.06437e+04 Fmax= 1.33677e+02, atom= 1223\n", + "Step= 414, Dmax= 2.4e-02 nm, Epot= -6.06437e+04 Fmax= 2.86011e+02, atom= 1223\n", + "Step= 415, Dmax= 2.9e-02 nm, Epot= -6.06508e+04 Fmax= 2.16489e+02, atom= 1223\n", + "Step= 417, Dmax= 1.7e-02 nm, Epot= -6.06582e+04 Fmax= 7.43573e+01, atom= 1223\n", + "Step= 418, Dmax= 2.1e-02 nm, Epot= -6.06584e+04 Fmax= 3.06738e+02, atom= 1223\n", + "Step= 419, Dmax= 2.5e-02 nm, Epot= -6.06699e+04 Fmax= 1.31746e+02, atom= 1223\n", + "Step= 421, Dmax= 1.5e-02 nm, Epot= -6.06743e+04 Fmax= 1.24125e+02, atom= 1223\n", + "Step= 422, Dmax= 1.8e-02 nm, Epot= -6.06772e+04 Fmax= 1.85336e+02, atom= 1223\n", + "Step= 423, Dmax= 2.2e-02 nm, Epot= -6.06812e+04 Fmax= 1.91020e+02, atom= 1223\n", + "Step= 424, Dmax= 2.6e-02 nm, Epot= -6.06825e+04 Fmax= 2.56809e+02, atom= 1223\n", + "Step= 425, Dmax= 3.1e-02 nm, Epot= -6.06852e+04 Fmax= 2.81063e+02, atom= 1223\n", + "Step= 427, Dmax= 1.9e-02 nm, Epot= -6.06969e+04 Fmax= 5.07303e+01, atom= 2326\n", + "Step= 428, Dmax= 2.2e-02 nm, Epot= -6.07028e+04 Fmax= 3.54027e+02, atom= 2326\n", + "Step= 429, Dmax= 2.7e-02 nm, Epot= -6.07137e+04 Fmax= 1.30348e+02, atom= 1223\n", + "Step= 431, Dmax= 1.6e-02 nm, Epot= -6.07179e+04 Fmax= 1.33923e+02, atom= 1223\n", + "Step= 432, Dmax= 1.9e-02 nm, Epot= -6.07204e+04 Fmax= 1.96251e+02, atom= 1223\n", + "Step= 433, Dmax= 2.3e-02 nm, Epot= -6.07244e+04 Fmax= 2.06369e+02, atom= 1223\n", + "Step= 434, Dmax= 2.8e-02 nm, Epot= -6.07254e+04 Fmax= 2.73626e+02, atom= 1223\n", + "Step= 435, Dmax= 3.4e-02 nm, Epot= -6.07282e+04 Fmax= 3.02467e+02, atom= 1223\n", + "Step= 437, Dmax= 2.0e-02 nm, Epot= -6.07402e+04 Fmax= 6.05849e+01, atom= 2326\n", + "Step= 438, Dmax= 2.4e-02 nm, Epot= -6.07457e+04 Fmax= 3.65725e+02, atom= 2326\n", + "Step= 439, Dmax= 2.9e-02 nm, Epot= -6.07549e+04 Fmax= 1.42202e+02, atom= 2326\n", + "Step= 441, Dmax= 1.7e-02 nm, Epot= -6.07592e+04 Fmax= 1.38473e+02, atom= 1223\n", + "Step= 442, Dmax= 2.1e-02 nm, Epot= -6.07611e+04 Fmax= 2.15298e+02, atom= 1223\n", + "Step= 443, Dmax= 2.5e-02 nm, Epot= -6.07657e+04 Fmax= 2.15387e+02, atom= 1223\n", + "Step= 445, Dmax= 1.5e-02 nm, Epot= -6.07728e+04 Fmax= 5.21423e+01, atom= 2326\n", + "Step= 446, Dmax= 1.8e-02 nm, Epot= -6.07796e+04 Fmax= 2.56476e+02, atom= 2326\n", + "Step= 447, Dmax= 2.2e-02 nm, Epot= -6.07864e+04 Fmax= 1.17198e+02, atom= 1223\n", + "Step= 449, Dmax= 1.3e-02 nm, Epot= -6.07907e+04 Fmax= 9.99643e+01, atom= 1223\n", + "Step= 450, Dmax= 1.6e-02 nm, Epot= -6.07940e+04 Fmax= 1.64265e+02, atom= 1223\n", + "Step= 451, Dmax= 1.9e-02 nm, Epot= -6.07984e+04 Fmax= 1.60225e+02, atom= 1223\n", + "Step= 452, Dmax= 2.2e-02 nm, Epot= -6.08005e+04 Fmax= 2.22581e+02, atom= 1223\n", + "Step= 453, Dmax= 2.7e-02 nm, Epot= -6.08042e+04 Fmax= 2.41085e+02, atom= 1223\n", + "Step= 454, Dmax= 3.2e-02 nm, Epot= -6.08045e+04 Fmax= 3.11641e+02, atom= 1223\n", + "Step= 455, Dmax= 3.9e-02 nm, Epot= -6.08066e+04 Fmax= 3.48347e+02, atom= 1223\n", + "Step= 457, Dmax= 2.3e-02 nm, Epot= -6.08208e+04 Fmax= 6.99340e+01, atom= 2326\n", + "Step= 458, Dmax= 2.8e-02 nm, Epot= -6.08238e+04 Fmax= 4.30790e+02, atom= 2326\n", + "Step= 459, Dmax= 3.4e-02 nm, Epot= -6.08347e+04 Fmax= 1.58143e+02, atom= 2326\n", + "Step= 461, Dmax= 2.0e-02 nm, Epot= -6.08390e+04 Fmax= 1.59487e+02, atom= 2327\n", + "Step= 462, Dmax= 2.4e-02 nm, Epot= -6.08398e+04 Fmax= 2.41392e+02, atom= 1223\n", + "Step= 463, Dmax= 2.9e-02 nm, Epot= -6.08440e+04 Fmax= 2.52208e+02, atom= 1223\n", + "Step= 465, Dmax= 1.7e-02 nm, Epot= -6.08533e+04 Fmax= 6.02601e+01, atom= 2326\n", + "Step= 466, Dmax= 2.1e-02 nm, Epot= -6.08591e+04 Fmax= 2.91071e+02, atom= 2326\n", + "Step= 467, Dmax= 2.5e-02 nm, Epot= -6.08663e+04 Fmax= 1.35117e+02, atom= 2326\n", + "Step= 469, Dmax= 1.5e-02 nm, Epot= -6.08708e+04 Fmax= 1.09440e+02, atom= 2327\n", + "Step= 470, Dmax= 1.8e-02 nm, Epot= -6.08733e+04 Fmax= 1.90966e+02, atom= 1223\n", + "Step= 471, Dmax= 2.2e-02 nm, Epot= -6.08780e+04 Fmax= 1.81492e+02, atom= 1223\n", + "Step= 472, Dmax= 2.6e-02 nm, Epot= -6.08789e+04 Fmax= 2.58389e+02, atom= 1223\n", + "Step= 473, Dmax= 3.1e-02 nm, Epot= -6.08827e+04 Fmax= 2.73250e+02, atom= 1223\n", + "Step= 475, Dmax= 1.9e-02 nm, Epot= -6.08927e+04 Fmax= 5.96241e+01, atom= 2326\n", + "Step= 476, Dmax= 2.2e-02 nm, Epot= -6.08978e+04 Fmax= 3.29611e+02, atom= 2326\n", + "Step= 477, Dmax= 2.7e-02 nm, Epot= -6.09063e+04 Fmax= 1.34986e+02, atom= 2326\n", + "Step= 479, Dmax= 1.6e-02 nm, Epot= -6.09107e+04 Fmax= 1.24750e+02, atom= 2327\n", + "Step= 480, Dmax= 1.9e-02 nm, Epot= -6.09128e+04 Fmax= 1.97233e+02, atom= 1223\n", + "Step= 481, Dmax= 2.3e-02 nm, Epot= -6.09170e+04 Fmax= 2.01198e+02, atom= 1223\n", + "Step= 482, Dmax= 2.8e-02 nm, Epot= -6.09176e+04 Fmax= 2.70444e+02, atom= 1223\n", + "Step= 483, Dmax= 3.3e-02 nm, Epot= -6.09205e+04 Fmax= 2.98919e+02, atom= 1223\n", + "Step= 485, Dmax= 2.0e-02 nm, Epot= -6.09324e+04 Fmax= 6.28237e+01, atom= 2326\n", + "Step= 486, Dmax= 2.4e-02 nm, Epot= -6.09374e+04 Fmax= 3.51108e+02, atom= 2326\n", + "Step= 487, Dmax= 2.9e-02 nm, Epot= -6.09460e+04 Fmax= 1.44706e+02, atom= 2326\n", + "Step= 489, Dmax= 1.7e-02 nm, Epot= -6.09503e+04 Fmax= 1.35641e+02, atom= 2327\n", + "Step= 490, Dmax= 2.1e-02 nm, Epot= -6.09523e+04 Fmax= 2.04670e+02, atom= 2327\n", + "Step= 491, Dmax= 2.5e-02 nm, Epot= -6.09560e+04 Fmax= 2.16173e+02, atom= 1223\n", + "Step= 493, Dmax= 1.5e-02 nm, Epot= -6.09637e+04 Fmax= 5.23354e+01, atom= 2326\n", + "Step= 494, Dmax= 1.8e-02 nm, Epot= -6.09703e+04 Fmax= 2.48278e+02, atom= 2326\n", + "Step= 495, Dmax= 2.2e-02 nm, Epot= -6.09767e+04 Fmax= 1.17648e+02, atom= 2326\n", + "Step= 497, Dmax= 1.3e-02 nm, Epot= -6.09810e+04 Fmax= 9.57970e+01, atom= 2327\n", + "Step= 498, Dmax= 1.6e-02 nm, Epot= -6.09842e+04 Fmax= 1.56906e+02, atom= 1223\n", + "Step= 499, Dmax= 1.9e-02 nm, Epot= -6.09882e+04 Fmax= 1.64292e+02, atom= 1223\n", + "Step= 500, Dmax= 2.2e-02 nm, Epot= -6.09903e+04 Fmax= 2.12035e+02, atom= 1223\n", + "Step= 501, Dmax= 2.7e-02 nm, Epot= -6.09931e+04 Fmax= 2.46997e+02, atom= 1223\n", + "Step= 502, Dmax= 3.2e-02 nm, Epot= -6.09936e+04 Fmax= 2.96341e+02, atom= 1223\n", + "Step= 503, Dmax= 3.9e-02 nm, Epot= -6.09937e+04 Fmax= 3.56965e+02, atom= 1223\n", + "Step= 505, Dmax= 2.3e-02 nm, Epot= -6.10108e+04 Fmax= 6.71921e+01, atom= 2326\n", + "Step= 506, Dmax= 2.8e-02 nm, Epot= -6.10157e+04 Fmax= 4.04859e+02, atom= 2326\n", + "Step= 507, Dmax= 3.3e-02 nm, Epot= -6.10247e+04 Fmax= 1.62177e+02, atom= 2326\n", + "Step= 509, Dmax= 2.0e-02 nm, Epot= -6.10290e+04 Fmax= 1.63104e+02, atom= 2327\n", + "Step= 510, Dmax= 2.4e-02 nm, Epot= -6.10306e+04 Fmax= 2.28723e+02, atom= 2327\n", + "Step= 511, Dmax= 2.9e-02 nm, Epot= -6.10336e+04 Fmax= 2.46947e+02, atom= 2327\n", + "Step= 513, Dmax= 1.7e-02 nm, Epot= -6.10428e+04 Fmax= 6.12178e+01, atom= 2326\n", + "Step= 514, Dmax= 2.1e-02 nm, Epot= -6.10473e+04 Fmax= 2.91723e+02, atom= 2326\n", + "Step= 515, Dmax= 2.5e-02 nm, Epot= -6.10550e+04 Fmax= 1.31883e+02, atom= 2326\n", + "Step= 517, Dmax= 1.5e-02 nm, Epot= -6.10593e+04 Fmax= 1.15556e+02, atom= 2327\n", + "Step= 518, Dmax= 1.8e-02 nm, Epot= -6.10619e+04 Fmax= 1.74574e+02, atom= 2327\n", + "Step= 519, Dmax= 2.2e-02 nm, Epot= -6.10655e+04 Fmax= 1.83451e+02, atom= 2327\n", + "Step= 520, Dmax= 2.6e-02 nm, Epot= -6.10659e+04 Fmax= 2.47827e+02, atom= 2327\n", + "Step= 521, Dmax= 3.1e-02 nm, Epot= -6.10684e+04 Fmax= 2.73296e+02, atom= 1223\n", + "Step= 523, Dmax= 1.9e-02 nm, Epot= -6.10802e+04 Fmax= 6.18504e+01, atom= 2326\n", + "Step= 524, Dmax= 2.2e-02 nm, Epot= -6.10843e+04 Fmax= 3.14941e+02, atom= 2326\n", + "Step= 525, Dmax= 2.7e-02 nm, Epot= -6.10925e+04 Fmax= 1.38163e+02, atom= 2326\n", + "Step= 527, Dmax= 1.6e-02 nm, Epot= -6.10968e+04 Fmax= 1.27977e+02, atom= 2327\n", + "Step= 528, Dmax= 1.9e-02 nm, Epot= -6.10990e+04 Fmax= 1.84856e+02, atom= 2327\n", + "Step= 529, Dmax= 2.3e-02 nm, Epot= -6.11021e+04 Fmax= 1.99339e+02, atom= 2327\n", + "Step= 531, Dmax= 1.4e-02 nm, Epot= -6.11093e+04 Fmax= 4.64262e+01, atom= 2326\n", + "Step= 532, Dmax= 1.7e-02 nm, Epot= -6.11156e+04 Fmax= 2.30252e+02, atom= 2326\n", + "Step= 533, Dmax= 2.0e-02 nm, Epot= -6.11221e+04 Fmax= 1.07528e+02, atom= 2326\n", + "Step= 535, Dmax= 1.2e-02 nm, Epot= -6.11259e+04 Fmax= 9.38625e+01, atom= 2327\n", + "Step= 536, Dmax= 1.4e-02 nm, Epot= -6.11291e+04 Fmax= 1.40430e+02, atom= 2327\n", + "Step= 537, Dmax= 1.7e-02 nm, Epot= -6.11325e+04 Fmax= 1.48252e+02, atom= 2327\n", + "Step= 538, Dmax= 2.1e-02 nm, Epot= -6.11340e+04 Fmax= 1.97714e+02, atom= 2327\n", + "Step= 539, Dmax= 2.5e-02 nm, Epot= -6.11365e+04 Fmax= 2.16855e+02, atom= 1223\n", + "Step= 541, Dmax= 1.5e-02 nm, Epot= -6.11456e+04 Fmax= 4.98271e+01, atom= 2326\n", + "Step= 542, Dmax= 1.8e-02 nm, Epot= -6.11506e+04 Fmax= 2.48533e+02, atom= 2326\n", + "Step= 543, Dmax= 2.2e-02 nm, Epot= -6.11577e+04 Fmax= 1.13798e+02, atom= 2326\n", + "Step= 545, Dmax= 1.3e-02 nm, Epot= -6.11615e+04 Fmax= 1.02535e+02, atom= 2327\n", + "Step= 546, Dmax= 1.5e-02 nm, Epot= -6.11641e+04 Fmax= 1.49348e+02, atom= 2327\n", + "Step= 547, Dmax= 1.9e-02 nm, Epot= -6.11672e+04 Fmax= 1.60635e+02, atom= 2327\n", + "Step= 548, Dmax= 2.2e-02 nm, Epot= -6.11681e+04 Fmax= 2.10958e+02, atom= 2327\n", + "Step= 549, Dmax= 2.7e-02 nm, Epot= -6.11699e+04 Fmax= 2.31711e+02, atom= 2327\n", + "Step= 551, Dmax= 1.6e-02 nm, Epot= -6.11808e+04 Fmax= 5.42368e+01, atom= 2326\n", + "Step= 552, Dmax= 1.9e-02 nm, Epot= -6.11837e+04 Fmax= 2.69126e+02, atom= 2326\n", + "Step= 553, Dmax= 2.3e-02 nm, Epot= -6.11920e+04 Fmax= 1.20699e+02, atom= 2326\n", + "Step= 555, Dmax= 1.4e-02 nm, Epot= -6.11958e+04 Fmax= 1.12091e+02, atom= 2327\n", + "Step= 556, Dmax= 1.7e-02 nm, Epot= -6.11980e+04 Fmax= 1.57795e+02, atom= 2327\n", + "Step= 557, Dmax= 2.0e-02 nm, Epot= -6.12007e+04 Fmax= 1.74921e+02, atom= 2327\n", + "Step= 558, Dmax= 2.4e-02 nm, Epot= -6.12009e+04 Fmax= 2.23417e+02, atom= 2327\n", + "Step= 559, Dmax= 2.9e-02 nm, Epot= -6.12016e+04 Fmax= 2.51672e+02, atom= 2327\n", + "Step= 561, Dmax= 1.7e-02 nm, Epot= -6.12149e+04 Fmax= 5.52209e+01, atom= 2326\n", + "Step= 562, Dmax= 2.1e-02 nm, Epot= -6.12168e+04 Fmax= 2.93120e+02, atom= 2326\n", + "Step= 563, Dmax= 2.5e-02 nm, Epot= -6.12263e+04 Fmax= 1.26087e+02, atom= 2326\n", + "Step= 565, Dmax= 1.5e-02 nm, Epot= -6.12300e+04 Fmax= 1.24136e+02, atom= 2327\n", + "Step= 566, Dmax= 1.8e-02 nm, Epot= -6.12320e+04 Fmax= 1.65719e+02, atom= 2327\n", + "Step= 567, Dmax= 2.1e-02 nm, Epot= -6.12341e+04 Fmax= 1.91486e+02, atom= 2327\n", + "Step= 568, Dmax= 2.6e-02 nm, Epot= -6.12342e+04 Fmax= 2.35788e+02, atom= 2327\n", + "Step= 570, Dmax= 1.5e-02 nm, Epot= -6.12457e+04 Fmax= 3.28485e+01, atom= 1949\n", + "Step= 571, Dmax= 1.9e-02 nm, Epot= -6.12528e+04 Fmax= 3.12952e+02, atom= 1949\n", + "Step= 572, Dmax= 2.2e-02 nm, Epot= -6.12635e+04 Fmax= 8.37420e+01, atom= 1949\n", + "Step= 574, Dmax= 1.3e-02 nm, Epot= -6.12669e+04 Fmax= 1.46378e+02, atom= 1949\n", + "Step= 575, Dmax= 1.6e-02 nm, Epot= -6.12704e+04 Fmax= 1.24146e+02, atom= 1949\n", + "Step= 576, Dmax= 1.9e-02 nm, Epot= -6.12724e+04 Fmax= 2.11671e+02, atom= 1949\n", + "Step= 577, Dmax= 2.3e-02 nm, Epot= -6.12763e+04 Fmax= 1.78723e+02, atom= 1949\n", + "Step= 579, Dmax= 1.4e-02 nm, Epot= -6.12815e+04 Fmax= 5.08404e+01, atom= 1949\n", + "Step= 580, Dmax= 1.7e-02 nm, Epot= -6.12853e+04 Fmax= 2.25402e+02, atom= 1949\n", + "Step= 581, Dmax= 2.0e-02 nm, Epot= -6.12922e+04 Fmax= 1.14717e+02, atom= 1949\n", + "Step= 583, Dmax= 1.2e-02 nm, Epot= -6.12957e+04 Fmax= 8.96617e+01, atom= 1949\n", + "Step= 584, Dmax= 1.4e-02 nm, Epot= -6.12986e+04 Fmax= 1.61616e+02, atom= 1949\n", + "Step= 585, Dmax= 1.7e-02 nm, Epot= -6.13024e+04 Fmax= 1.31872e+02, atom= 1949\n", + "Step= 586, Dmax= 2.1e-02 nm, Epot= -6.13036e+04 Fmax= 2.31553e+02, atom= 1949\n", + "Step= 587, Dmax= 2.5e-02 nm, Epot= -6.13080e+04 Fmax= 1.89964e+02, atom= 1949\n", + "Step= 589, Dmax= 1.5e-02 nm, Epot= -6.13136e+04 Fmax= 5.63080e+01, atom= 1949\n", + "Step= 590, Dmax= 1.8e-02 nm, Epot= -6.13161e+04 Fmax= 2.41869e+02, atom= 1949\n", + "Step= 591, Dmax= 2.1e-02 nm, Epot= -6.13239e+04 Fmax= 1.23513e+02, atom= 1949\n", + "Step= 593, Dmax= 1.3e-02 nm, Epot= -6.13275e+04 Fmax= 9.63505e+01, atom= 1949\n", + "Step= 594, Dmax= 1.5e-02 nm, Epot= -6.13300e+04 Fmax= 1.73277e+02, atom= 1949\n", + "Step= 595, Dmax= 1.9e-02 nm, Epot= -6.13339e+04 Fmax= 1.42028e+02, atom= 1949\n", + "Step= 596, Dmax= 2.2e-02 nm, Epot= -6.13347e+04 Fmax= 2.48073e+02, atom= 1949\n", + "Step= 597, Dmax= 2.7e-02 nm, Epot= -6.13392e+04 Fmax= 2.04293e+02, atom= 1949\n", + "Step= 599, Dmax= 1.6e-02 nm, Epot= -6.13453e+04 Fmax= 5.91080e+01, atom= 1949\n", + "Step= 600, Dmax= 1.9e-02 nm, Epot= -6.13467e+04 Fmax= 2.61541e+02, atom= 1949\n", + "Step= 601, Dmax= 2.3e-02 nm, Epot= -6.13554e+04 Fmax= 1.30293e+02, atom= 1949\n", + "Step= 603, Dmax= 1.4e-02 nm, Epot= -6.13590e+04 Fmax= 1.05596e+02, atom= 1949\n", + "Step= 604, Dmax= 1.7e-02 nm, Epot= -6.13612e+04 Fmax= 1.83230e+02, atom= 1949\n", + "Step= 605, Dmax= 2.0e-02 nm, Epot= -6.13651e+04 Fmax= 1.54879e+02, atom= 1949\n", + "Step= 606, Dmax= 2.4e-02 nm, Epot= -6.13653e+04 Fmax= 2.63165e+02, atom= 1949\n", + "Step= 607, Dmax= 2.9e-02 nm, Epot= -6.13698e+04 Fmax= 2.21558e+02, atom= 1949\n", + "Step= 609, Dmax= 1.7e-02 nm, Epot= -6.13767e+04 Fmax= 6.02873e+01, atom= 1949\n", + "Step= 611, Dmax= 1.0e-02 nm, Epot= -6.13804e+04 Fmax= 1.15753e+02, atom= 1949\n", + "Step= 612, Dmax= 1.2e-02 nm, Epot= -6.13838e+04 Fmax= 9.54349e+01, atom= 1949\n", + "Step= 613, Dmax= 1.5e-02 nm, Epot= -6.13864e+04 Fmax= 1.54037e+02, atom= 1949\n", + "Step= 614, Dmax= 1.8e-02 nm, Epot= -6.13899e+04 Fmax= 1.50894e+02, atom= 1949\n", + "Step= 615, Dmax= 2.1e-02 nm, Epot= -6.13913e+04 Fmax= 2.07060e+02, atom= 1949\n", + "Step= 616, Dmax= 2.6e-02 nm, Epot= -6.13939e+04 Fmax= 2.35138e+02, atom= 1949\n", + "Step= 617, Dmax= 3.1e-02 nm, Epot= -6.13943e+04 Fmax= 2.78445e+02, atom= 1949\n", + "Step= 619, Dmax= 1.8e-02 nm, Epot= -6.14049e+04 Fmax= 2.74896e+01, atom= 3323\n", + "Step= 620, Dmax= 2.2e-02 nm, Epot= -6.14121e+04 Fmax= 3.33049e+02, atom= 3323\n", + "Step= 621, Dmax= 2.7e-02 nm, Epot= -6.14272e+04 Fmax= 1.25677e+02, atom= 1949\n", + "Step= 623, Dmax= 1.6e-02 nm, Epot= -6.14299e+04 Fmax= 1.41946e+02, atom= 1949\n", + "Step= 624, Dmax= 1.9e-02 nm, Epot= -6.14319e+04 Fmax= 1.91541e+02, atom= 1949\n", + "Step= 625, Dmax= 2.3e-02 nm, Epot= -6.14346e+04 Fmax= 1.97188e+02, atom= 1949\n", + "Step= 627, Dmax= 1.4e-02 nm, Epot= -6.14412e+04 Fmax= 3.12574e+01, atom= 3323\n", + "Step= 628, Dmax= 1.7e-02 nm, Epot= -6.14471e+04 Fmax= 2.47294e+02, atom= 1949\n", + "Step= 629, Dmax= 2.0e-02 nm, Epot= -6.14568e+04 Fmax= 9.19825e+01, atom= 1949\n", + "Step= 631, Dmax= 1.2e-02 nm, Epot= -6.14598e+04 Fmax= 1.09206e+02, atom= 1949\n", + "Step= 632, Dmax= 1.4e-02 nm, Epot= -6.14627e+04 Fmax= 1.36560e+02, atom= 1949\n", + "Step= 633, Dmax= 1.7e-02 nm, Epot= -6.14654e+04 Fmax= 1.53138e+02, atom= 1949\n", + "Step= 634, Dmax= 2.1e-02 nm, Epot= -6.14674e+04 Fmax= 2.01566e+02, atom= 1949\n", + "Step= 635, Dmax= 2.5e-02 nm, Epot= -6.14699e+04 Fmax= 2.13372e+02, atom= 1949\n", + "Step= 637, Dmax= 1.5e-02 nm, Epot= -6.14770e+04 Fmax= 3.05146e+01, atom= 3323\n", + "Step= 638, Dmax= 1.8e-02 nm, Epot= -6.14823e+04 Fmax= 2.71011e+02, atom= 1949\n", + "Step= 639, Dmax= 2.1e-02 nm, Epot= -6.14939e+04 Fmax= 9.39666e+01, atom= 1949\n", + "Step= 641, Dmax= 1.3e-02 nm, Epot= -6.14968e+04 Fmax= 1.21082e+02, atom= 1949\n", + "Step= 642, Dmax= 1.5e-02 nm, Epot= -6.14997e+04 Fmax= 1.42449e+02, atom= 1949\n", + "Step= 643, Dmax= 1.8e-02 nm, Epot= -6.15021e+04 Fmax= 1.67905e+02, atom= 1949\n", + "Step= 644, Dmax= 2.2e-02 nm, Epot= -6.15040e+04 Fmax= 2.12542e+02, atom= 1949\n", + "Step= 645, Dmax= 2.7e-02 nm, Epot= -6.15060e+04 Fmax= 2.31949e+02, atom= 1949\n", + "Step= 647, Dmax= 1.6e-02 nm, Epot= -6.15144e+04 Fmax= 3.02890e+01, atom= 3323\n", + "Step= 648, Dmax= 1.9e-02 nm, Epot= -6.15187e+04 Fmax= 2.87664e+02, atom= 1949\n", + "Step= 649, Dmax= 2.3e-02 nm, Epot= -6.15322e+04 Fmax= 1.07222e+02, atom= 1949\n", + "Step= 651, Dmax= 1.4e-02 nm, Epot= -6.15352e+04 Fmax= 1.23671e+02, atom= 1949\n", + "Step= 652, Dmax= 1.7e-02 nm, Epot= -6.15376e+04 Fmax= 1.60224e+02, atom= 1949\n", + "Step= 653, Dmax= 2.0e-02 nm, Epot= -6.15403e+04 Fmax= 1.73212e+02, atom= 1949\n", + "Step= 654, Dmax= 2.4e-02 nm, Epot= -6.15413e+04 Fmax= 2.36454e+02, atom= 1949\n", + "Step= 655, Dmax= 2.9e-02 nm, Epot= -6.15439e+04 Fmax= 2.40930e+02, atom= 1949\n", + "Step= 657, Dmax= 1.7e-02 nm, Epot= -6.15530e+04 Fmax= 3.99922e+01, atom= 3323\n", + "Step= 659, Dmax= 1.0e-02 nm, Epot= -6.15576e+04 Fmax= 1.33768e+02, atom= 1949\n", + "Step= 660, Dmax= 1.2e-02 nm, Epot= -6.15620e+04 Fmax= 7.56548e+01, atom= 1949\n", + "Step= 661, Dmax= 1.5e-02 nm, Epot= -6.15640e+04 Fmax= 1.71268e+02, atom= 1949\n", + "Step= 662, Dmax= 1.8e-02 nm, Epot= -6.15687e+04 Fmax= 1.29578e+02, atom= 1949\n", + "Step= 664, Dmax= 1.1e-02 nm, Epot= -6.15731e+04 Fmax= 5.24324e+01, atom= 1949\n", + "Step= 665, Dmax= 1.3e-02 nm, Epot= -6.15767e+04 Fmax= 1.67527e+02, atom= 1949\n", + "Step= 666, Dmax= 1.5e-02 nm, Epot= -6.15815e+04 Fmax= 9.30733e+01, atom= 1949\n", + "Step= 667, Dmax= 1.8e-02 nm, Epot= -6.15824e+04 Fmax= 2.25481e+02, atom= 1949\n", + "Step= 668, Dmax= 2.2e-02 nm, Epot= -6.15882e+04 Fmax= 1.47792e+02, atom= 1949\n", + "Step= 670, Dmax= 1.3e-02 nm, Epot= -6.15926e+04 Fmax= 7.13658e+01, atom= 1949\n", + "Step= 671, Dmax= 1.6e-02 nm, Epot= -6.15947e+04 Fmax= 1.92535e+02, atom= 1949\n", + "Step= 672, Dmax= 1.9e-02 nm, Epot= -6.16001e+04 Fmax= 1.28400e+02, atom= 1949\n", + "Step= 674, Dmax= 1.1e-02 nm, Epot= -6.16041e+04 Fmax= 6.58039e+01, atom= 1949\n", + "Step= 675, Dmax= 1.4e-02 nm, Epot= -6.16072e+04 Fmax= 1.69507e+02, atom= 1949\n", + "Step= 676, Dmax= 1.7e-02 nm, Epot= -6.16117e+04 Fmax= 1.09017e+02, atom= 1949\n", + "Step= 677, Dmax= 2.0e-02 nm, Epot= -6.16123e+04 Fmax= 2.32233e+02, atom= 1949\n", + "Step= 678, Dmax= 2.4e-02 nm, Epot= -6.16177e+04 Fmax= 1.67062e+02, atom= 1949\n", + "Step= 680, Dmax= 1.4e-02 nm, Epot= -6.16228e+04 Fmax= 6.73887e+01, atom= 1949\n", + "Step= 681, Dmax= 1.7e-02 nm, Epot= -6.16243e+04 Fmax= 2.15799e+02, atom= 1949\n", + "Step= 682, Dmax= 2.1e-02 nm, Epot= -6.16309e+04 Fmax= 1.28582e+02, atom= 1949\n", + "Step= 684, Dmax= 1.2e-02 nm, Epot= -6.16349e+04 Fmax= 7.97385e+01, atom= 1949\n", + "Step= 685, Dmax= 1.5e-02 nm, Epot= -6.16372e+04 Fmax= 1.72885e+02, atom= 1949\n", + "Step= 686, Dmax= 1.8e-02 nm, Epot= -6.16416e+04 Fmax= 1.25784e+02, atom= 1949\n", + "Step= 687, Dmax= 2.1e-02 nm, Epot= -6.16417e+04 Fmax= 2.40575e+02, atom= 1949\n", + "Step= 688, Dmax= 2.6e-02 nm, Epot= -6.16469e+04 Fmax= 1.87556e+02, atom= 1949\n", + "Step= 690, Dmax= 1.5e-02 nm, Epot= -6.16529e+04 Fmax= 6.60799e+01, atom= 3323\n", + "Step= 691, Dmax= 1.8e-02 nm, Epot= -6.16537e+04 Fmax= 2.40106e+02, atom= 3323\n", + "Step= 692, Dmax= 2.2e-02 nm, Epot= -6.16616e+04 Fmax= 1.29555e+02, atom= 3323\n", + "Step= 694, Dmax= 1.3e-02 nm, Epot= -6.16654e+04 Fmax= 9.36283e+01, atom= 3323\n", + "Step= 695, Dmax= 1.6e-02 nm, Epot= -6.16674e+04 Fmax= 1.74793e+02, atom= 3323\n", + "Step= 696, Dmax= 1.9e-02 nm, Epot= -6.16715e+04 Fmax= 1.46095e+02, atom= 3323\n", + "Step= 698, Dmax= 1.1e-02 nm, Epot= -6.16762e+04 Fmax= 4.50594e+01, atom= 3323\n", + "Step= 699, Dmax= 1.4e-02 nm, Epot= -6.16805e+04 Fmax= 1.84908e+02, atom= 3323\n", + "Step= 700, Dmax= 1.6e-02 nm, Epot= -6.16862e+04 Fmax= 9.14170e+01, atom= 3323\n", + "Step= 702, Dmax= 9.9e-03 nm, Epot= -6.16895e+04 Fmax= 7.54193e+01, atom= 3323\n", + "Step= 703, Dmax= 1.2e-02 nm, Epot= -6.16926e+04 Fmax= 1.24684e+02, atom= 3323\n", + "Step= 704, Dmax= 1.4e-02 nm, Epot= -6.16961e+04 Fmax= 1.14940e+02, atom= 3323\n", + "Step= 705, Dmax= 1.7e-02 nm, Epot= -6.16980e+04 Fmax= 1.74170e+02, atom= 3323\n", + "Step= 706, Dmax= 2.1e-02 nm, Epot= -6.17014e+04 Fmax= 1.70701e+02, atom= 3323\n", + "Step= 707, Dmax= 2.5e-02 nm, Epot= -6.17016e+04 Fmax= 2.46551e+02, atom= 3323\n", + "Step= 708, Dmax= 3.0e-02 nm, Epot= -6.17043e+04 Fmax= 2.49177e+02, atom= 3323\n", + "Step= 710, Dmax= 1.8e-02 nm, Epot= -6.17140e+04 Fmax= 4.56564e+01, atom= 3323\n", + "Step= 711, Dmax= 2.1e-02 nm, Epot= -6.17147e+04 Fmax= 3.10156e+02, atom= 3323\n", + "Step= 712, Dmax= 2.6e-02 nm, Epot= -6.17275e+04 Fmax= 1.18057e+02, atom= 3323\n", + "Step= 714, Dmax= 1.5e-02 nm, Epot= -6.17303e+04 Fmax= 1.40059e+02, atom= 3323\n", + "Step= 715, Dmax= 1.8e-02 nm, Epot= -6.17327e+04 Fmax= 1.69299e+02, atom= 3323\n", + "Step= 716, Dmax= 2.2e-02 nm, Epot= -6.17346e+04 Fmax= 2.00894e+02, atom= 3323\n", + "Step= 717, Dmax= 2.6e-02 nm, Epot= -6.17358e+04 Fmax= 2.46036e+02, atom= 3323\n", + "Step= 718, Dmax= 3.2e-02 nm, Epot= -6.17362e+04 Fmax= 2.85767e+02, atom= 3323\n", + "Step= 720, Dmax= 1.9e-02 nm, Epot= -6.17488e+04 Fmax= 3.10433e+01, atom= 3323\n", + "Step= 721, Dmax= 2.3e-02 nm, Epot= -6.17512e+04 Fmax= 3.54161e+02, atom= 3323\n", + "Step= 722, Dmax= 2.7e-02 nm, Epot= -6.17691e+04 Fmax= 1.10459e+02, atom= 3323\n", + "Step= 724, Dmax= 1.6e-02 nm, Epot= -6.17708e+04 Fmax= 1.67762e+02, atom= 3323\n", + "Step= 725, Dmax= 2.0e-02 nm, Epot= -6.17742e+04 Fmax= 1.65501e+02, atom= 3323\n", + "Step= 727, Dmax= 1.2e-02 nm, Epot= -6.17800e+04 Fmax= 3.57628e+01, atom= 3323\n", + "Step= 728, Dmax= 1.4e-02 nm, Epot= -6.17848e+04 Fmax= 2.05701e+02, atom= 3323\n", + "Step= 729, Dmax= 1.7e-02 nm, Epot= -6.17919e+04 Fmax= 8.54245e+01, atom= 3323\n", + "Step= 731, Dmax= 1.0e-02 nm, Epot= -6.17950e+04 Fmax= 8.67985e+01, atom= 3323\n", + "Step= 732, Dmax= 1.2e-02 nm, Epot= -6.17978e+04 Fmax= 1.21109e+02, atom= 3323\n", + "Step= 733, Dmax= 1.5e-02 nm, Epot= -6.18008e+04 Fmax= 1.27346e+02, atom= 3323\n", + "Step= 734, Dmax= 1.8e-02 nm, Epot= -6.18025e+04 Fmax= 1.70965e+02, atom= 3323\n", + "Step= 735, Dmax= 2.1e-02 nm, Epot= -6.18049e+04 Fmax= 1.87542e+02, atom= 3323\n", + "Step= 736, Dmax= 2.5e-02 nm, Epot= -6.18051e+04 Fmax= 2.40863e+02, atom= 3323\n", + "Step= 737, Dmax= 3.1e-02 nm, Epot= -6.18060e+04 Fmax= 2.76327e+02, atom= 3323\n", + "Step= 739, Dmax= 1.8e-02 nm, Epot= -6.18181e+04 Fmax= 3.75260e+01, atom= 3323\n", + "Step= 741, Dmax= 1.1e-02 nm, Epot= -6.18229e+04 Fmax= 1.43857e+02, atom= 3323\n", + "Step= 742, Dmax= 1.3e-02 nm, Epot= -6.18272e+04 Fmax= 8.13268e+01, atom= 3323\n", + "Step= 743, Dmax= 1.6e-02 nm, Epot= -6.18282e+04 Fmax= 1.86414e+02, atom= 3323\n", + "Step= 744, Dmax= 1.9e-02 nm, Epot= -6.18330e+04 Fmax= 1.36189e+02, atom= 3323\n", + "Step= 746, Dmax= 1.1e-02 nm, Epot= -6.18373e+04 Fmax= 5.46422e+01, atom= 3323\n", + "Step= 747, Dmax= 1.4e-02 nm, Epot= -6.18394e+04 Fmax= 1.77559e+02, atom= 3323\n", + "Step= 748, Dmax= 1.6e-02 nm, Epot= -6.18449e+04 Fmax= 9.81546e+01, atom= 3323\n", + "Step= 750, Dmax= 9.9e-03 nm, Epot= -6.18481e+04 Fmax= 6.92657e+01, atom= 3323\n", + "Step= 751, Dmax= 1.2e-02 nm, Epot= -6.18505e+04 Fmax= 1.29277e+02, atom= 3323\n", + "Step= 752, Dmax= 1.4e-02 nm, Epot= -6.18538e+04 Fmax= 1.11387e+02, atom= 3323\n", + "Step= 753, Dmax= 1.7e-02 nm, Epot= -6.18547e+04 Fmax= 1.76156e+02, atom= 3323\n", + "Step= 754, Dmax= 2.0e-02 nm, Epot= -6.18577e+04 Fmax= 1.69428e+02, atom= 3323\n", + "Step= 756, Dmax= 1.2e-02 nm, Epot= -6.18638e+04 Fmax= 3.54448e+01, atom= 3323\n", + "Step= 757, Dmax= 1.5e-02 nm, Epot= -6.18662e+04 Fmax= 2.16367e+02, atom= 3323\n", + "Step= 758, Dmax= 1.8e-02 nm, Epot= -6.18749e+04 Fmax= 8.04779e+01, atom= 3323\n", + "Step= 760, Dmax= 1.1e-02 nm, Epot= -6.18775e+04 Fmax= 9.98588e+01, atom= 3323\n", + "Step= 761, Dmax= 1.3e-02 nm, Epot= -6.18799e+04 Fmax= 1.13861e+02, atom= 3323\n", + "Step= 762, Dmax= 1.5e-02 nm, Epot= -6.18816e+04 Fmax= 1.44921e+02, atom= 3323\n", + "Step= 763, Dmax= 1.8e-02 nm, Epot= -6.18834e+04 Fmax= 1.63846e+02, atom= 3323\n", + "Step= 764, Dmax= 2.2e-02 nm, Epot= -6.18835e+04 Fmax= 2.07417e+02, atom= 3323\n", + "Step= 765, Dmax= 2.6e-02 nm, Epot= -6.18839e+04 Fmax= 2.38270e+02, atom= 3323\n", + "Step= 767, Dmax= 1.6e-02 nm, Epot= -6.18959e+04 Fmax= 3.25907e+01, atom= 3323\n", + "Step= 769, Dmax= 9.5e-03 nm, Epot= -6.18999e+04 Fmax= 1.23018e+02, atom= 3323\n", + "Step= 770, Dmax= 1.1e-02 nm, Epot= -6.19041e+04 Fmax= 7.19840e+01, atom= 3323\n", + "Step= 771, Dmax= 1.4e-02 nm, Epot= -6.19044e+04 Fmax= 1.58267e+02, atom= 3323\n", + "Step= 772, Dmax= 1.6e-02 nm, Epot= -6.19089e+04 Fmax= 1.21307e+02, atom= 3323\n", + "Step= 774, Dmax= 9.8e-03 nm, Epot= -6.19134e+04 Fmax= 4.35690e+01, atom= 3323\n", + "Step= 775, Dmax= 1.2e-02 nm, Epot= -6.19146e+04 Fmax= 1.59358e+02, atom= 3323\n", + "Step= 776, Dmax= 1.4e-02 nm, Epot= -6.19206e+04 Fmax= 7.88613e+01, atom= 3323\n", + "Step= 778, Dmax= 8.5e-03 nm, Epot= -6.19235e+04 Fmax= 6.66403e+01, atom= 3323\n", + "Step= 779, Dmax= 1.0e-02 nm, Epot= -6.19255e+04 Fmax= 1.04174e+02, atom= 3323\n", + "Step= 780, Dmax= 1.2e-02 nm, Epot= -6.19282e+04 Fmax= 1.04693e+02, atom= 3323\n", + "Step= 781, Dmax= 1.5e-02 nm, Epot= -6.19292e+04 Fmax= 1.42981e+02, atom= 3323\n", + "Step= 782, Dmax= 1.8e-02 nm, Epot= -6.19310e+04 Fmax= 1.57064e+02, atom= 1040\n", + "Step= 784, Dmax= 1.1e-02 nm, Epot= -6.19380e+04 Fmax= 2.27104e+01, atom= 1040\n", + "Step= 785, Dmax= 1.3e-02 nm, Epot= -6.19430e+04 Fmax= 1.90449e+02, atom= 1040\n", + "Step= 786, Dmax= 1.5e-02 nm, Epot= -6.19515e+04 Fmax= 6.69500e+01, atom= 1040\n", + "Step= 788, Dmax= 9.1e-03 nm, Epot= -6.19538e+04 Fmax= 8.98881e+01, atom= 1040\n", + "Step= 789, Dmax= 1.1e-02 nm, Epot= -6.19563e+04 Fmax= 9.69127e+01, atom= 1040\n", + "Step= 790, Dmax= 1.3e-02 nm, Epot= -6.19578e+04 Fmax= 1.27878e+02, atom= 1040\n", + "Step= 791, Dmax= 1.6e-02 nm, Epot= -6.19599e+04 Fmax= 1.41222e+02, atom= 1040\n", + "Step= 792, Dmax= 1.9e-02 nm, Epot= -6.19601e+04 Fmax= 1.82178e+02, atom= 1040\n", + "Step= 793, Dmax= 2.3e-02 nm, Epot= -6.19612e+04 Fmax= 2.05354e+02, atom= 1040\n", + "Step= 795, Dmax= 1.4e-02 nm, Epot= -6.19711e+04 Fmax= 2.85714e+01, atom= 1040\n", + "Step= 796, Dmax= 1.6e-02 nm, Epot= -6.19713e+04 Fmax= 2.54575e+02, atom= 1040\n", + "Step= 797, Dmax= 2.0e-02 nm, Epot= -6.19841e+04 Fmax= 8.58721e+01, atom= 1040\n", + "Step= 799, Dmax= 1.2e-02 nm, Epot= -6.19861e+04 Fmax= 1.15620e+02, atom= 1040\n", + "Step= 800, Dmax= 1.4e-02 nm, Epot= -6.19883e+04 Fmax= 1.26179e+02, atom= 1040\n", + "Step= 801, Dmax= 1.7e-02 nm, Epot= -6.19892e+04 Fmax= 1.63102e+02, atom= 1040\n", + "Step= 802, Dmax= 2.0e-02 nm, Epot= -6.19906e+04 Fmax= 1.84593e+02, atom= 1040\n", + "Step= 804, Dmax= 1.2e-02 nm, Epot= -6.19983e+04 Fmax= 2.27677e+01, atom= 1040\n", + "Step= 805, Dmax= 1.5e-02 nm, Epot= -6.20034e+04 Fmax= 2.24568e+02, atom= 1040\n", + "Step= 806, Dmax= 1.8e-02 nm, Epot= -6.20131e+04 Fmax= 7.26377e+01, atom= 1040\n", + "Step= 808, Dmax= 1.1e-02 nm, Epot= -6.20151e+04 Fmax= 1.09182e+02, atom= 1040\n", + "Step= 809, Dmax= 1.3e-02 nm, Epot= -6.20177e+04 Fmax= 1.06686e+02, atom= 1040\n", + "Step= 810, Dmax= 1.5e-02 nm, Epot= -6.20186e+04 Fmax= 1.52878e+02, atom= 1040\n", + "Step= 811, Dmax= 1.8e-02 nm, Epot= -6.20209e+04 Fmax= 1.57619e+02, atom= 1040\n", + "Step= 813, Dmax= 1.1e-02 nm, Epot= -6.20268e+04 Fmax= 2.99193e+01, atom= 1040\n", + "Step= 814, Dmax= 1.3e-02 nm, Epot= -6.20296e+04 Fmax= 1.94079e+02, atom= 1040\n", + "Step= 815, Dmax= 1.6e-02 nm, Epot= -6.20371e+04 Fmax= 7.75292e+01, atom= 1040\n", + "Step= 817, Dmax= 9.5e-03 nm, Epot= -6.20396e+04 Fmax= 8.38311e+01, atom= 1040\n", + "Step= 818, Dmax= 1.1e-02 nm, Epot= -6.20416e+04 Fmax= 1.10206e+02, atom= 1040\n", + "Step= 819, Dmax= 1.4e-02 nm, Epot= -6.20438e+04 Fmax= 1.21578e+02, atom= 1040\n", + "Step= 820, Dmax= 1.6e-02 nm, Epot= -6.20449e+04 Fmax= 1.57570e+02, atom= 1040\n", + "Step= 821, Dmax= 2.0e-02 nm, Epot= -6.20464e+04 Fmax= 1.76421e+02, atom= 1040\n", + "Step= 823, Dmax= 1.2e-02 nm, Epot= -6.20535e+04 Fmax= 3.59349e+01, atom= 1782\n", + "Step= 824, Dmax= 1.4e-02 nm, Epot= -6.20582e+04 Fmax= 1.45222e+02, atom= 1040\n", + "Step= 825, Dmax= 1.7e-02 nm, Epot= -6.20607e+04 Fmax= 1.46283e+02, atom= 1040\n", + "Step= 827, Dmax= 1.0e-02 nm, Epot= -6.20664e+04 Fmax= 4.02890e+01, atom= 1782\n", + "Step= 828, Dmax= 1.2e-02 nm, Epot= -6.20708e+04 Fmax= 1.11162e+02, atom= 1040\n", + "Step= 829, Dmax= 1.5e-02 nm, Epot= -6.20723e+04 Fmax= 1.37422e+02, atom= 1040\n", + "Step= 830, Dmax= 1.8e-02 nm, Epot= -6.20734e+04 Fmax= 1.63267e+02, atom= 1040\n", + "Step= 831, Dmax= 2.1e-02 nm, Epot= -6.20738e+04 Fmax= 1.96144e+02, atom= 1040\n", + "Step= 833, Dmax= 1.3e-02 nm, Epot= -6.20834e+04 Fmax= 4.40350e+01, atom= 1782\n", + "Step= 834, Dmax= 1.5e-02 nm, Epot= -6.20886e+04 Fmax= 1.03352e+02, atom= 1040\n", + "Step= 836, Dmax= 9.1e-03 nm, Epot= -6.20925e+04 Fmax= 5.41424e+01, atom= 1040\n", + "Step= 837, Dmax= 1.1e-02 nm, Epot= -6.20932e+04 Fmax= 1.32904e+02, atom= 4937\n", + "Step= 838, Dmax= 1.3e-02 nm, Epot= -6.20977e+04 Fmax= 9.61326e+01, atom= 4937\n", + "Step= 840, Dmax= 7.9e-03 nm, Epot= -6.21014e+04 Fmax= 4.11376e+01, atom= 4937\n", + "Step= 841, Dmax= 9.4e-03 nm, Epot= -6.21036e+04 Fmax= 1.17201e+02, atom= 4937\n", + "Step= 842, Dmax= 1.1e-02 nm, Epot= -6.21076e+04 Fmax= 7.87920e+01, atom= 4937\n", + "Step= 844, Dmax= 6.8e-03 nm, Epot= -6.21105e+04 Fmax= 3.82117e+01, atom= 4937\n", + "Step= 845, Dmax= 8.2e-03 nm, Epot= -6.21129e+04 Fmax= 1.06706e+02, atom= 4937\n", + "Step= 846, Dmax= 9.8e-03 nm, Epot= -6.21165e+04 Fmax= 6.35798e+01, atom= 4937\n", + "Step= 847, Dmax= 1.2e-02 nm, Epot= -6.21170e+04 Fmax= 1.42991e+02, atom= 4937\n", + "Step= 848, Dmax= 1.4e-02 nm, Epot= -6.21211e+04 Fmax= 1.03213e+02, atom= 4937\n", + "Step= 850, Dmax= 8.5e-03 nm, Epot= -6.21246e+04 Fmax= 4.43484e+01, atom= 4937\n", + "Step= 851, Dmax= 1.0e-02 nm, Epot= -6.21266e+04 Fmax= 1.25828e+02, atom= 4937\n", + "Step= 852, Dmax= 1.2e-02 nm, Epot= -6.21303e+04 Fmax= 8.48035e+01, atom= 4937\n", + "Step= 854, Dmax= 7.3e-03 nm, Epot= -6.21333e+04 Fmax= 4.11273e+01, atom= 4937\n", + "Step= 855, Dmax= 8.8e-03 nm, Epot= -6.21354e+04 Fmax= 1.14631e+02, atom= 4937\n", + "Step= 856, Dmax= 1.1e-02 nm, Epot= -6.21390e+04 Fmax= 6.88454e+01, atom= 4937\n", + "Step= 857, Dmax= 1.3e-02 nm, Epot= -6.21392e+04 Fmax= 1.53268e+02, atom= 4937\n", + "Step= 858, Dmax= 1.5e-02 nm, Epot= -6.21433e+04 Fmax= 1.12028e+02, atom= 4937\n", + "Step= 860, Dmax= 9.1e-03 nm, Epot= -6.21469e+04 Fmax= 4.66405e+01, atom= 4937\n", + "Step= 861, Dmax= 1.1e-02 nm, Epot= -6.21487e+04 Fmax= 1.36129e+02, atom= 4937\n", + "Step= 862, Dmax= 1.3e-02 nm, Epot= -6.21526e+04 Fmax= 9.02350e+01, atom= 4937\n", + "Step= 864, Dmax= 7.9e-03 nm, Epot= -6.21554e+04 Fmax= 4.53374e+01, atom= 4937\n", + "Step= 865, Dmax= 9.4e-03 nm, Epot= -6.21574e+04 Fmax= 1.21818e+02, atom= 4937\n", + "Step= 866, Dmax= 1.1e-02 nm, Epot= -6.21610e+04 Fmax= 7.56580e+01, atom= 4937\n", + "Step= 868, Dmax= 6.8e-03 nm, Epot= -6.21636e+04 Fmax= 4.35774e+01, atom= 4937\n", + "Step= 869, Dmax= 8.1e-03 nm, Epot= -6.21661e+04 Fmax= 9.42887e+01, atom= 4937\n", + "Step= 870, Dmax= 9.8e-03 nm, Epot= -6.21688e+04 Fmax= 7.59747e+01, atom= 4937\n", + "Step= 871, Dmax= 1.2e-02 nm, Epot= -6.21700e+04 Fmax= 1.25936e+02, atom= 4937\n", + "Step= 872, Dmax= 1.4e-02 nm, Epot= -6.21728e+04 Fmax= 1.18387e+02, atom= 4937\n", + "Step= 874, Dmax= 8.4e-03 nm, Epot= -6.21767e+04 Fmax= 2.82705e+01, atom= 4937\n", + "Step= 875, Dmax= 1.0e-02 nm, Epot= -6.21796e+04 Fmax= 1.55920e+02, atom= 4937\n", + "Step= 876, Dmax= 1.2e-02 nm, Epot= -6.21851e+04 Fmax= 5.99825e+01, atom= 4937\n", + "Step= 878, Dmax= 7.3e-03 nm, Epot= -6.21875e+04 Fmax= 6.96112e+01, atom= 4937\n", + "Step= 879, Dmax= 8.8e-03 nm, Epot= -6.21897e+04 Fmax= 8.14074e+01, atom= 4937\n", + "Step= 880, Dmax= 1.1e-02 nm, Epot= -6.21917e+04 Fmax= 1.02919e+02, atom= 4937\n", + "Step= 881, Dmax= 1.3e-02 nm, Epot= -6.21937e+04 Fmax= 1.16141e+02, atom= 4937\n", + "Step= 882, Dmax= 1.5e-02 nm, Epot= -6.21949e+04 Fmax= 1.48130e+02, atom= 4937\n", + "Step= 883, Dmax= 1.8e-02 nm, Epot= -6.21960e+04 Fmax= 1.68631e+02, atom= 4937\n", + "Step= 884, Dmax= 2.2e-02 nm, Epot= -6.21961e+04 Fmax= 2.10300e+02, atom= 4937\n", + "Step= 886, Dmax= 1.3e-02 nm, Epot= -6.22052e+04 Fmax= 2.65702e+01, atom= 4938\n", + "Step= 887, Dmax= 1.6e-02 nm, Epot= -6.22084e+04 Fmax= 2.46009e+02, atom= 4938\n", + "Step= 888, Dmax= 1.9e-02 nm, Epot= -6.22175e+04 Fmax= 9.12969e+01, atom= 4937\n", + "Step= 890, Dmax= 1.1e-02 nm, Epot= -6.22197e+04 Fmax= 1.10043e+02, atom= 4937\n", + "Step= 891, Dmax= 1.4e-02 nm, Epot= -6.22214e+04 Fmax= 1.25301e+02, atom= 4937\n", + "Step= 892, Dmax= 1.6e-02 nm, Epot= -6.22226e+04 Fmax= 1.60125e+02, atom= 4937\n", + "Step= 893, Dmax= 2.0e-02 nm, Epot= -6.22236e+04 Fmax= 1.81383e+02, atom= 4937\n", + "Step= 895, Dmax= 1.2e-02 nm, Epot= -6.22309e+04 Fmax= 2.21315e+01, atom= 4937\n", + "Step= 896, Dmax= 1.4e-02 nm, Epot= -6.22382e+04 Fmax= 1.89503e+02, atom= 4937\n", + "Step= 897, Dmax= 1.7e-02 nm, Epot= -6.22443e+04 Fmax= 9.73893e+01, atom= 4937\n", + "Step= 899, Dmax= 1.0e-02 nm, Epot= -6.22471e+04 Fmax= 8.18655e+01, atom= 4937\n", + "Step= 900, Dmax= 1.2e-02 nm, Epot= -6.22482e+04 Fmax= 1.29203e+02, atom= 4937\n", + "Step= 901, Dmax= 1.5e-02 nm, Epot= -6.22506e+04 Fmax= 1.25820e+02, atom= 4937\n", + "Step= 903, Dmax= 8.7e-03 nm, Epot= -6.22551e+04 Fmax= 2.63156e+01, atom= 4937\n", + "Step= 904, Dmax= 1.0e-02 nm, Epot= -6.22592e+04 Fmax= 1.47918e+02, atom= 938\n", + "Step= 905, Dmax= 1.3e-02 nm, Epot= -6.22643e+04 Fmax= 7.25947e+01, atom= 938\n", + "Step= 907, Dmax= 7.6e-03 nm, Epot= -6.22668e+04 Fmax= 6.09570e+01, atom= 938\n", + "Step= 908, Dmax= 9.1e-03 nm, Epot= -6.22689e+04 Fmax= 9.46149e+01, atom= 938\n", + "Step= 909, Dmax= 1.1e-02 nm, Epot= -6.22712e+04 Fmax= 9.64365e+01, atom= 938\n", + "Step= 910, Dmax= 1.3e-02 nm, Epot= -6.22726e+04 Fmax= 1.30240e+02, atom= 938\n", + "Step= 911, Dmax= 1.6e-02 nm, Epot= -6.22743e+04 Fmax= 1.43357e+02, atom= 938\n", + "Step= 912, Dmax= 1.9e-02 nm, Epot= -6.22745e+04 Fmax= 1.85040e+02, atom= 938\n", + "Step= 913, Dmax= 2.3e-02 nm, Epot= -6.22748e+04 Fmax= 2.06568e+02, atom= 938\n", + "Step= 915, Dmax= 1.4e-02 nm, Epot= -6.22848e+04 Fmax= 2.89039e+01, atom= 939\n", + "Step= 916, Dmax= 1.6e-02 nm, Epot= -6.22867e+04 Fmax= 2.56133e+02, atom= 938\n", + "Step= 917, Dmax= 1.9e-02 nm, Epot= -6.22971e+04 Fmax= 9.03164e+01, atom= 938\n", + "Step= 919, Dmax= 1.2e-02 nm, Epot= -6.22990e+04 Fmax= 1.16369e+02, atom= 938\n", + "Step= 920, Dmax= 1.4e-02 nm, Epot= -6.23012e+04 Fmax= 1.25718e+02, atom= 938\n", + "Step= 921, Dmax= 1.7e-02 nm, Epot= -6.23022e+04 Fmax= 1.67778e+02, atom= 938\n", + "Step= 922, Dmax= 2.0e-02 nm, Epot= -6.23039e+04 Fmax= 1.83211e+02, atom= 938\n", + "Step= 924, Dmax= 1.2e-02 nm, Epot= -6.23098e+04 Fmax= 2.97891e+01, atom= 938\n", + "Step= 925, Dmax= 1.5e-02 nm, Epot= -6.23118e+04 Fmax= 2.12365e+02, atom= 938\n", + "Step= 926, Dmax= 1.7e-02 nm, Epot= -6.23196e+04 Fmax= 9.45052e+01, atom= 938\n", + "Step= 928, Dmax= 1.0e-02 nm, Epot= -6.23222e+04 Fmax= 8.84470e+01, atom= 9387\n", + "Step= 929, Dmax= 1.3e-02 nm, Epot= -6.23230e+04 Fmax= 1.31686e+02, atom= 938\n", + "Step= 930, Dmax= 1.5e-02 nm, Epot= -6.23255e+04 Fmax= 1.31326e+02, atom= 938\n", + "Step= 932, Dmax= 9.1e-03 nm, Epot= -6.23301e+04 Fmax= 2.91377e+01, atom= 2427\n", + "Step= 933, Dmax= 1.1e-02 nm, Epot= -6.23324e+04 Fmax= 1.65391e+02, atom= 2427\n", + "Step= 934, Dmax= 1.3e-02 nm, Epot= -6.23384e+04 Fmax= 6.71878e+01, atom= 2427\n", + "Step= 936, Dmax= 7.8e-03 nm, Epot= -6.23406e+04 Fmax= 6.66937e+01, atom= 4937\n", + "Step= 937, Dmax= 9.4e-03 nm, Epot= -6.23422e+04 Fmax= 9.63323e+01, atom= 4937\n", + "Step= 938, Dmax= 1.1e-02 nm, Epot= -6.23444e+04 Fmax= 1.01690e+02, atom= 4937\n", + "Step= 939, Dmax= 1.4e-02 nm, Epot= -6.23452e+04 Fmax= 1.34622e+02, atom= 4937\n", + "Step= 940, Dmax= 1.6e-02 nm, Epot= -6.23470e+04 Fmax= 1.49160e+02, atom= 4937\n", + "Step= 942, Dmax= 9.7e-03 nm, Epot= -6.23527e+04 Fmax= 2.66976e+01, atom= 2427\n", + "Step= 943, Dmax= 1.2e-02 nm, Epot= -6.23557e+04 Fmax= 1.79183e+02, atom= 2427\n", + "Step= 944, Dmax= 1.4e-02 nm, Epot= -6.23619e+04 Fmax= 7.03322e+01, atom= 4937\n", + "Step= 946, Dmax= 8.4e-03 nm, Epot= -6.23641e+04 Fmax= 7.98115e+01, atom= 4937\n", + "Step= 947, Dmax= 1.0e-02 nm, Epot= -6.23660e+04 Fmax= 9.62597e+01, atom= 4937\n", + "Step= 948, Dmax= 1.2e-02 nm, Epot= -6.23678e+04 Fmax= 1.17195e+02, atom= 4937\n", + "Step= 949, Dmax= 1.5e-02 nm, Epot= -6.23691e+04 Fmax= 1.38279e+02, atom= 4937\n", + "Step= 950, Dmax= 1.7e-02 nm, Epot= -6.23703e+04 Fmax= 1.67205e+02, atom= 4937\n", + "Step= 951, Dmax= 2.1e-02 nm, Epot= -6.23704e+04 Fmax= 2.01543e+02, atom= 4937\n", + "Step= 952, Dmax= 2.5e-02 nm, Epot= -6.23709e+04 Fmax= 2.35760e+02, atom= 4937\n", + "Step= 954, Dmax= 1.5e-02 nm, Epot= -6.23809e+04 Fmax= 4.28066e+01, atom= 4938\n", + "Step= 956, Dmax= 9.0e-03 nm, Epot= -6.23838e+04 Fmax= 1.01697e+02, atom= 4232\n", + "Step= 957, Dmax= 1.1e-02 nm, Epot= -6.23862e+04 Fmax= 8.75414e+01, atom= 4937\n", + "Step= 958, Dmax= 1.3e-02 nm, Epot= -6.23872e+04 Fmax= 1.43666e+02, atom= 4937\n", + "Step= 959, Dmax= 1.6e-02 nm, Epot= -6.23897e+04 Fmax= 1.32980e+02, atom= 4937\n", + "Step= 961, Dmax= 9.4e-03 nm, Epot= -6.23936e+04 Fmax= 3.15960e+01, atom= 4937\n", + "Step= 962, Dmax= 1.1e-02 nm, Epot= -6.23977e+04 Fmax= 1.50721e+02, atom= 4937\n", + "Step= 963, Dmax= 1.3e-02 nm, Epot= -6.24016e+04 Fmax= 8.27897e+01, atom= 4937\n", + "Step= 965, Dmax= 8.1e-03 nm, Epot= -6.24039e+04 Fmax= 5.95661e+01, atom= 4937\n", + "Step= 966, Dmax= 9.7e-03 nm, Epot= -6.24059e+04 Fmax= 1.11909e+02, atom= 4937\n", + "Step= 967, Dmax= 1.2e-02 nm, Epot= -6.24085e+04 Fmax= 9.38756e+01, atom= 4937\n", + "Step= 968, Dmax= 1.4e-02 nm, Epot= -6.24096e+04 Fmax= 1.52476e+02, atom= 4937\n", + "Step= 969, Dmax= 1.7e-02 nm, Epot= -6.24120e+04 Fmax= 1.45137e+02, atom= 4937\n", + "Step= 970, Dmax= 2.0e-02 nm, Epot= -6.24121e+04 Fmax= 2.07900e+02, atom= 4937\n", + "Step= 971, Dmax= 2.4e-02 nm, Epot= -6.24135e+04 Fmax= 2.21125e+02, atom= 4937\n", + "Step= 973, Dmax= 1.5e-02 nm, Epot= -6.24210e+04 Fmax= 3.03283e+01, atom= 4937\n", + "Step= 974, Dmax= 1.7e-02 nm, Epot= -6.24262e+04 Fmax= 2.34137e+02, atom= 4937\n", + "Step= 975, Dmax= 2.1e-02 nm, Epot= -6.24323e+04 Fmax= 1.23070e+02, atom= 4937\n", + "Step= 977, Dmax= 1.3e-02 nm, Epot= -6.24349e+04 Fmax= 1.03752e+02, atom= 4937\n", + "Step= 978, Dmax= 1.5e-02 nm, Epot= -6.24363e+04 Fmax= 1.55823e+02, atom= 4937\n", + "Step= 979, Dmax= 1.8e-02 nm, Epot= -6.24382e+04 Fmax= 1.64005e+02, atom= 4937\n", + "Step= 980, Dmax= 2.2e-02 nm, Epot= -6.24387e+04 Fmax= 2.12617e+02, atom= 4937\n", + "Step= 981, Dmax= 2.6e-02 nm, Epot= -6.24391e+04 Fmax= 2.46961e+02, atom= 4937\n", + "Step= 982, Dmax= 3.1e-02 nm, Epot= -6.24392e+04 Fmax= 2.92519e+02, atom= 4937\n", + "Step= 984, Dmax= 1.9e-02 nm, Epot= -6.24498e+04 Fmax= 5.74096e+01, atom= 4938\n", + "Step= 986, Dmax= 1.1e-02 nm, Epot= -6.24524e+04 Fmax= 1.25219e+02, atom= 4232\n", + "Step= 987, Dmax= 1.3e-02 nm, Epot= -6.24548e+04 Fmax= 1.09413e+02, atom= 4232\n", + "Step= 988, Dmax= 1.6e-02 nm, Epot= -6.24557e+04 Fmax= 1.79087e+02, atom= 4232\n", + "Step= 989, Dmax= 1.9e-02 nm, Epot= -6.24583e+04 Fmax= 1.57637e+02, atom= 4232\n", + "Step= 991, Dmax= 1.2e-02 nm, Epot= -6.24624e+04 Fmax= 4.41992e+01, atom= 4937\n", + "Step= 992, Dmax= 1.4e-02 nm, Epot= -6.24650e+04 Fmax= 1.84347e+02, atom= 4937\n", + "Step= 993, Dmax= 1.7e-02 nm, Epot= -6.24693e+04 Fmax= 1.04549e+02, atom= 4937\n", + "Step= 995, Dmax= 1.0e-02 nm, Epot= -6.24717e+04 Fmax= 7.27234e+01, atom= 4937\n", + "Step= 996, Dmax= 1.2e-02 nm, Epot= -6.24734e+04 Fmax= 1.39498e+02, atom= 4937\n", + "Step= 997, Dmax= 1.4e-02 nm, Epot= -6.24759e+04 Fmax= 1.17886e+02, atom= 4937\n", + "Step= 998, Dmax= 1.7e-02 nm, Epot= -6.24766e+04 Fmax= 1.89061e+02, atom= 4232\n", + "Step= 999, Dmax= 2.1e-02 nm, Epot= -6.24787e+04 Fmax= 1.80077e+02, atom= 4937\n", + "Step= 1000, Dmax= 2.5e-02 nm, Epot= -6.24779e+04 Fmax= 2.64158e+02, atom= 4232\n", + "Energy minimization reached the maximum number of steps before the forces\n", + "reached the requested precision Fmax < 10.\n", + "\n", + "writing lowest energy coordinates.\n", + "\n", + "Back Off! I just backed up em.pdb to ./#em.pdb.1#\n", + "\n", + "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", + "Potential Energy = -6.2478738e+04\n", + "Maximum force = 1.8007661e+02 on atom 4937\n", + "Norm of force = 5.3058659e+00\n", + "\n", + "GROMACS reminds you: \"The greatest shortcoming of the human race is our inability to understand the exponential function.\" (Albert Bartlett)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Everybody Lie Down On the Floor and Keep Calm\" (KLF)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] All files set up for a run time of 1000 ps (dt=0.01, nsteps=100000)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 2008514542\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.125 nm, buffer size 0.025 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.100 nm, buffer size 0.000 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'struct': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro',\n", + " 'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top',\n", + " '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top']}" + ] + }, + "execution_count": 44, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from mdpow.equil import OctanolSimulation\n", + "\n", + "oct_sim = OctanolSimulation(\n", + " molecule=\"BENZ\",\n", + " forcefield=MARTINI,\n", + " mdp={\n", + " \"energy_minimize\": str(EM_FILE.absolute()),\n", + " \"MD_relaxed\": str(EQ_FILE.absolute()),\n", + " \"MD_NPT\": str(EQ_FILE.absolute()),\n", + " \"MD_restrained\": str(RUN_FILE.absolute()),\n", + " },\n", + " distance=4.0,\n", + ")\n", + "oct_sim.topology(str(BENZENE_ITP))\n", + "oct_sim.solvate(struct=MARTINI_BENZENE, maxwarn=1)\n", + "oct_sim.energy_minimize(maxwarn=1)\n", + "oct_sim.MD_relaxed(runtime=1e3, dt=0.01)" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 10 to 50, rlist from 1.1 to 1.228\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the GPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "100000 steps, 1000.0 ps (continuing from step 100000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 100000, remaining wall clock time: 0 s \n", + "NOTE: 31 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.128 0.032 398.5\n", + " (ns/day) (hour/ns)\n", + "Performance: 26.842 0.894\n", + "\n", + "GROMACS reminds you: \"Everybody Lie Down On the Floor and Keep Calm\" (KLF)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + }, + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 45, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "r = gromacs.run.MDrunner(\n", + " dirname=oct_sim.dirs[\"MD_relaxed\"],\n", + " deffnm=\"md\",\n", + " c=\"md.pdb\",\n", + " cpi=True,\n", + " v=True,\n", + ")\n", + "r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.equil : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro').\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 't']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -t /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "Last frame -1 time 1000.000 \n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"It was something to at least have a choice of nightmares\" (Joseph Conrad)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] All files set up for a run time of 10000 ps (dt=0.02, nsteps=500000)\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -33575937\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.167 nm, buffer size 0.067 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.108 nm, buffer size 0.008 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "Reading Coordinates, Velocities and Box size from old trajectory\n", + "\n", + "Will read whole trajectory\n", + "\n", + "Using frame at t = 1000 ps\n", + "\n", + "Starting time for run is 0 ps\n", + "\n", + "This run will generate roughly 15 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 10 to 25, rlist from 1.108 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the GPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "500000 steps, 10000.0 ps (continuing from step 500000, 10000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 500000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.060 0.015 397.1\n", + " (ns/day) (hour/ns)\n", + "Performance: 114.104 0.210\n", + "\n", + "GROMACS reminds you: \"Your Country Needs YOU\" (U.S. Army)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + }, + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 46, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "oct_sim.MD(\n", + " runtime=1e4, qscript=[\"local.sh\"], dt=0.02\n", + ")\n", + "\n", + "r = gromacs.run.MDrunner(\n", + " dirname=oct_sim.dirs[\"MD_NPT\"], deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True\n", + ")\n", + "r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 47, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.gro').\n", + "/home/awsm/MDPOW/mdpow/fep.py:596: UserWarning: Directory 'FEP/octanol' already exists --- will overwrite existing files.\n", + " warnings.warn(wmsg)\n", + "mdpow.fep : WARNING Directory 'FEP/octanol' already exists --- will overwrite existing files.\n", + "mdpow.fep : INFO Solvation free energy calculation for molecule BENZ in solvent octanol.\n", + "mdpow.fep : INFO Base directory is '/home/awsm/MDPOW/doc/examples/martini'\n", + "mdpow.fep : INFO Using setup directories under 'FEP/octanol': {'coulomb': 'FEP/octanol/Coulomb', 'vdw': 'FEP/octanol/VDW'}\n", + "mdpow.fep : INFO Default checkpoint file is '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep'\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Microsecond Here I Come\" (P.J. Van Maaren)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.25\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1989017199\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Microsecond Here I Come\" (P.J. Van Maaren)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1346895930\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"If everything seems under control, you're just not going fast enough.\" (Mario Andretti)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -478482449\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"If everything seems under control, you're just not going fast enough.\" (Mario Andretti)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 2145386303\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The soul? There's nothing but chemistry here\" (Breaking Bad)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [coulomb] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Preparing vdw for lambda=0\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -67141633\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The soul? There's nothing but chemistry here\" (Breaking Bad)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.05\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1247367\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Bring Out the Gimp\" (Pulp Fiction)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.1\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -438780993\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Space May Be the Final Frontier, But It's Made in a Hollywood Basement\" (Red Hot Chili Peppers)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.2\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -806387971\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Space May Be the Final Frontier, But It's Made in a Hollywood Basement\" (Red Hot Chili Peppers)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.3\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -608984233\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Let's Unzip And Let's Unfold\" (Red Hot Chili Peppers)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.4\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -102383660\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Let's Unzip And Let's Unfold\" (Red Hot Chili Peppers)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1946023915\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A Pretty Village Burning Makes a Pretty Fire\" (David Sandstrom)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.6\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1091582337\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A Pretty Village Burning Makes a Pretty Fire\" (David Sandstrom)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.65\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 989822767\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I don't want to achieve immortality through my work... I want to achieve it through not dying!\" (Woody Allen)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.7\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -33818753\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"There are three kinds of men. The one that learns by reading. The few who learn by observation. The rest of them have to pee on the electric fence for themselves.\" (Will Rogers)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1074663713\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"There are three kinds of men. The one that learns by reading. The few who learn by observation. The rest of them have to pee on the electric fence for themselves.\" (Will Rogers)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.8\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1106905097\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Trying is the first step towards failure.\" (Homer Simpson)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.85\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1090936833\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Trying is the first step towards failure.\" (Homer Simpson)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.9\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1511798142\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"All that glitters may not be gold, but at least it contains free electrons.\" (John Desmond Baernal)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.95\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -33820819\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"All that glitters may not be gold, but at least it contains free electrons.\" (John Desmond Baernal)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -6356998\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 2 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"You can get into a habit of thought in which you enjoy making fun of all those other people who don't see things as clearly as you do. We have to guard carefully against it.\" (Carl Sagan)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [vdw] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Saved state information to '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep'; reload later with G = Goct(filename='/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep').\n", + "mdpow.fep : INFO Finished setting up all individual simulations. Now run them...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1861188408\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top'],\n", + " 'maxwarn': 1,\n", + " 'couple-intramol': 'no',\n", + " 'couple_lambda0': 'vdw',\n", + " 'couple_lambda1': 'none',\n", + " 'sc_alpha': 0.5,\n", + " 'sc_power': 1,\n", + " 'sc_sigma': 0.3,\n", + " 'separate-dhdl-file': 'no',\n", + " 'ref_t': 300.0,\n", + " 'gen_temp': 300.0,\n", + " 'free_energy': 'yes',\n", + " 'couple_moltype': 'BENZ',\n", + " 'init_lambda_state': 15,\n", + " 'fep_lambdas': array([0. , 0.05, 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.65, 0.7 , 0.75,\n", + " 0.8 , 0.85, 0.9 , 0.95, 1. ]),\n", + " 'calc_lambda_neighbors': -1}" + ] + }, + "execution_count": 47, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "goct = mdpow.fep.Goct(simulation=oct_sim, runtime=1e+3, mdp=str(RUN_FILE.absolute()))\n", + "goct.setup(dt=0.02)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "These lambda windows take about twice as long as the water calculations on the author's desktop machine." + ] + }, + { + "cell_type": "code", + "execution_count": 48, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.177 to 1.221\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.058 0.015 398.7\n", + " (ns/day) (hour/ns)\n", + "Performance: 118.985 0.202\n", + "\n", + "GROMACS reminds you: \"Chemistry: It tends to be a messy science.\" (Gunnar von Heijne, former chair of the Nobel Committee for chemistry)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.058 0.015 398.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 118.740 0.202\n", + "\n", + "GROMACS reminds you: \"We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation.\" (Joseph Gay-Lussac, 1808)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.063 0.016 398.7\n", + " (ns/day) (hour/ns)\n", + "Performance: 109.130 0.220\n", + "\n", + "GROMACS reminds you: \"We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation.\" (Joseph Gay-Lussac, 1808)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.055 0.014 394.1\n", + " (ns/day) (hour/ns)\n", + "Performance: 124.605 0.193\n", + "\n", + "GROMACS reminds you: \"...sometimes a scream is better than a thesis.\" (Ralph Waldo Emerson)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.068 0.017 398.7\n", + " (ns/day) (hour/ns)\n", + "Performance: 100.751 0.238\n", + "\n", + "GROMACS reminds you: \"Have a Nice Day\" (R. McDonald)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 16 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.069 0.017 398.8\n", + " (ns/day) (hour/ns)\n", + "Performance: 99.759 0.241\n", + "\n", + "GROMACS reminds you: \"I wanted to make a clever chemistry joke, but the best ones Argon.\" (39.948)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.078 0.020 399.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 88.427 0.271\n", + "\n", + "GROMACS reminds you: \"I wanted to make a clever chemistry joke, but the best ones Argon.\" (39.948)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.061 0.015 398.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 113.755 0.211\n", + "\n", + "GROMACS reminds you: \"Science progresses best when observations force us to alter our preconceptions.\" (Vera Rubin)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.061 0.015 398.7\n", + " (ns/day) (hour/ns)\n", + "Performance: 112.992 0.212\n", + "\n", + "GROMACS reminds you: \"There is no place like ~\" (Anonymous)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 11 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.073 0.018 398.9\n", + " (ns/day) (hour/ns)\n", + "Performance: 94.679 0.253\n", + "\n", + "GROMACS reminds you: \"Academia is kind of like applied Marxism. The workers really do own the means of production.\" (Niklas Blomberg)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.084 0.021 399.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 82.075 0.292\n", + "\n", + "GROMACS reminds you: \"Academia is kind of like applied Marxism. The workers really do own the means of production.\" (Niklas Blomberg)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.054 0.013 398.5\n", + " (ns/day) (hour/ns)\n", + "Performance: 128.290 0.187\n", + "\n", + "GROMACS reminds you: \"My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)\" (Gogol Bordello)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 44 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.141 0.035 399.4\n", + " (ns/day) (hour/ns)\n", + "Performance: 48.911 0.491\n", + "\n", + "GROMACS reminds you: \"For the first time we can now mechanically simulate the cognitive process. We can make studies in artificial intelligence. Beyond that, this mechanism can be used to assist humans in learning. As we are going to have more mature students in greater numbers as time goes on, this type of teaching will probably be increasingly important.\" (Sister Mary Kenneth Keller)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.057 0.014 398.7\n", + " (ns/day) (hour/ns)\n", + "Performance: 120.860 0.199\n", + "\n", + "GROMACS reminds you: \"After a few talks we usually sit down to do some work... or drinking.\" (Mike Klein)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 12 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.088 0.022 396.5\n", + " (ns/day) (hour/ns)\n", + "Performance: 77.863 0.308\n", + "\n", + "GROMACS reminds you: \"After a few talks we usually sit down to do some work... or drinking.\" (Mike Klein)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.054 0.014 398.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 127.768 0.188\n", + "\n", + "GROMACS reminds you: \"Step On the Brakes\" (2 Unlimited)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 23 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.072 0.018 398.9\n", + " (ns/day) (hour/ns)\n", + "Performance: 95.165 0.252\n", + "\n", + "GROMACS reminds you: \"Here's the Way It Might End\" (G. Michael)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.064 0.016 398.7\n", + " (ns/day) (hour/ns)\n", + "Performance: 107.736 0.223\n", + "\n", + "GROMACS reminds you: \"As we all know, blinking lights means science.\" (Joss Whedon)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.059 0.015 398.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 116.516 0.206\n", + "\n", + "GROMACS reminds you: \"This is Tense !\" (Star Wars Episode I The Phantom Menace)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 20 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.067 0.017 398.8\n", + " (ns/day) (hour/ns)\n", + "Performance: 103.547 0.232\n", + "\n", + "GROMACS reminds you: \"This is Tense !\" (Star Wars Episode I The Phantom Menace)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.056 0.014 392.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 119.907 0.200\n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + } + ], + "source": [ + "for dir_ in goct.fep_dirs():\n", + " r = gromacs.run.MDrunner(\n", + " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=True\n", + " )\n", + " r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 49, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [FEP/octanol] Converting EDR -> XVG.bz2\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 200 time 800.000 mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 60 time 240.000 " + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 200 time 800.000 " + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO Analysis stride is 1.\n", + "mdpow.fep : INFO Analysis starts from frame 0.\n", + "mdpow.fep : INFO Analysis stops at frame None.\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg.bz2'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Finding dgdl xvg files, reading with stride=1 permissive=False.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0000\n", + "\u001b[32m2023-09-04 22:41:16.809\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.812\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 15.84.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.813\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 312.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 7.9840.\n", + "mdpow.fep : INFO The data are subsampled every 8 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0250\n", + "\u001b[32m2023-09-04 22:41:16.884\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.887\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 19.32.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.888\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 250.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.9640.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0500\n", + "\u001b[32m2023-09-04 22:41:16.961\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.963\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.68.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.963\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0750\n", + "\u001b[32m2023-09-04 22:41:17.036\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.038\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 26.28.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.039\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 185.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 13.4649.\n", + "mdpow.fep : INFO The data are subsampled every 14 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 1000\n", + "\u001b[32m2023-09-04 22:41:17.113\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.118\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.10.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.119\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.9740.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0000\n", + "\u001b[32m2023-09-04 22:41:17.331\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.333\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.09.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.333\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0050\n", + "\u001b[32m2023-09-04 22:41:17.543\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.545\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 24.34.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.546\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 200.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.4550.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0100\n", + "\u001b[32m2023-09-04 22:41:17.800\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.802\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.81.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.802\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0200\n", + "\u001b[32m2023-09-04 22:41:18.078\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.081\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 30.67.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.082\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 161.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 15.4720.\n", + "mdpow.fep : INFO The data are subsampled every 16 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0300\n", + "\u001b[32m2023-09-04 22:41:18.295\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.296\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.93.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.297\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.4728.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0400\n", + "\u001b[32m2023-09-04 22:41:18.511\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.512\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.32.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.513\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.4728.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0500\n", + "\u001b[32m2023-09-04 22:41:18.731\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.732\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.77.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.733\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0600\n", + "\u001b[32m2023-09-04 22:41:18.942\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.943\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.68.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.944\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0650\n", + "\u001b[32m2023-09-04 22:41:19.168\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.169\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.03.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.170\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0700\n", + "\u001b[32m2023-09-04 22:41:19.399\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.400\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.22.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.401\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0750\n", + "\u001b[32m2023-09-04 22:41:19.637\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.638\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.34.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.639\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0800\n", + "\u001b[32m2023-09-04 22:41:19.853\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.854\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.97.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.855\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.4728.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0850\n", + "\u001b[32m2023-09-04 22:41:20.088\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.089\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.34.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.090\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0900\n", + "\u001b[32m2023-09-04 22:41:20.323\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.324\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.22.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.325\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0950\n", + "\u001b[32m2023-09-04 22:41:20.541\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.542\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.59.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.543\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 1000\n", + "\u001b[32m2023-09-04 22:41:20.771\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.772\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.95.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.775\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.4728.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/pymbar/other_estimators.py:510: RuntimeWarning: invalid value encountered in sqrt\n", + " dDeltaF = np.sqrt(variance)\n", + "mdpow.fep : INFO DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n", + "mdpow.fep : INFO [BENZ] Octanol solvation free energy (coulomb) 0 (nan) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Octanol solvation free energy (vdw) 6.69992 (0.20) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Octanol solvation free energy (Gibbs) -6.69992 (nan) kJ/mol\n" + ] + }, + { + "data": { + "text/plain": [ + "-6.69992 (nan)" + ] + }, + "execution_count": 49, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "goct.convert_edr()\n", + "goct.analyze_alchemlyb()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Results\n", + "\n", + "Finally, we can compare the calculated free energies of solvation, taking the difference to find the free energy of transfer and then converting to a partition coefficient." + ] + }, + { + "cell_type": "code", + "execution_count": 50, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [BENZ] transfer free energy water --> octanol calculation\n", + "mdpow.fep : INFO The solvent is water .\n", + "mdpow.fep : INFO Using already calculated free energy DeltaA\n", + "mdpow.fep : INFO The solvent is octanol .\n", + "mdpow.fep : INFO Using already calculated free energy DeltaA\n", + "mdpow.fep : INFO [BENZ] Values at T = 300 K\n", + "mdpow.fep : INFO [BENZ] Free energy of transfer water --> octanol: -13.445 (nan) kJ/mol\n", + "mdpow.fep : INFO [BENZ] log P_ow: 2.341 (nan)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "log P_ow = 2.340869841742325 ± nan\n" + ] + } + ], + "source": [ + "delta_G, p_OW = mdpow.fep.pOW(gwat, goct)\n", + "print(f\"log P_ow = {p_OW.value} ± {p_OW.error}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The actual value is $\\log P_{ow} \\approx 2.13$." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "mdpow", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.5" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/doc/examples/martini/octanol.gro b/doc/examples/martini/octanol.gro new file mode 100644 index 00000000..bb3ce99e --- /dev/null +++ b/doc/examples/martini/octanol.gro @@ -0,0 +1,2253 @@ +Pure octanol + 2250 + 1OCO C1 1 1.824 0.076 0.199 0.0618 0.2052 0.0121 + 1OCO C2 2 2.064 0.141 0.520 -0.0505 -0.2708 -0.0128 + 1OCO PC 3 2.257 0.059 0.805 -0.0562 -0.2722 0.1350 + 2OCO C1 4 5.251 4.499 3.331 -0.0973 -0.0187 0.0399 + 2OCO C2 5 5.023 4.805 3.217 0.1660 -0.1214 0.1725 + 2OCO PC 6 4.689 4.829 3.104 0.1782 -0.1422 -0.0748 + 3OCO C1 7 0.160 5.908 2.025 -0.1836 0.1014 0.3046 + 3OCO C2 8 -0.118 6.190 2.041 -0.5981 0.0533 -0.0065 + 3OCO PC 9 -0.430 6.307 2.030 -0.0349 -0.0549 -0.1394 + 4OCO C1 10 3.920 4.493 0.188 0.5033 0.3729 0.1313 + 4OCO C2 11 3.773 4.141 0.295 -0.0245 -0.2722 0.1527 + 4OCO PC 12 3.548 3.938 0.451 -0.2254 0.7314 0.2228 + 5OCO C1 13 0.852 5.574 3.740 0.1963 -0.0800 -0.1686 + 5OCO C2 14 0.953 5.866 3.952 0.1544 -0.3576 -0.2373 + 5OCO PC 15 1.147 6.084 4.075 0.1998 0.0061 -0.0012 + 6OCO C1 16 3.576 2.907 2.999 -0.1417 -0.1663 0.1072 + 6OCO C2 17 3.864 2.601 2.880 -0.0148 0.2670 -0.2266 + 6OCO PC 18 4.164 2.360 2.940 0.1726 0.0506 0.4044 + 7OCO C1 19 5.878 1.713 1.458 -0.0261 0.1289 -0.0861 + 7OCO C2 20 6.207 1.842 1.357 0.0056 0.0498 0.0551 + 7OCO PC 21 6.318 2.024 1.070 -0.0353 -0.2536 0.0113 + 8OCO C1 22 3.074 4.741 2.488 -0.2672 0.0493 0.1003 + 8OCO C2 23 3.462 4.675 2.306 -0.2145 0.0439 0.0535 + 8OCO PC 24 3.801 4.714 2.219 -0.1092 0.1228 -0.3694 + 9OCO C1 25 1.533 4.969 3.752 0.2045 -0.2900 0.0658 + 9OCO C2 26 1.713 4.708 3.586 -0.2754 0.0384 -0.1305 + 9OCO PC 27 1.737 4.389 3.533 0.2107 -0.3352 -0.0968 + 10OCO C1 28 0.881 4.496 4.998 0.6254 -0.0063 -0.4146 + 10OCO C2 29 0.939 4.265 5.281 0.0469 -0.5451 -0.1035 + 10OCO PC 30 0.777 4.104 5.530 0.1143 -0.1211 0.0915 + 11OCO C1 31 5.035 0.329 3.438 0.0673 0.0942 -0.1248 + 11OCO C2 32 4.718 0.221 3.629 0.0533 0.1866 -0.2008 + 11OCO PC 33 4.379 0.171 3.636 0.3094 0.1958 0.1927 + 12OCO C1 34 4.417 5.540 0.516 0.5221 -0.2380 0.6708 + 12OCO C2 35 4.801 5.469 0.446 0.1006 0.3033 -0.2558 + 12OCO PC 36 5.064 5.422 0.286 -0.2500 -0.0583 0.2587 + 13OCO C1 37 1.548 3.664 0.400 -0.2536 -0.0732 -0.0713 + 13OCO C2 38 1.783 3.615 0.119 0.2356 -0.4315 0.3733 + 13OCO PC 39 1.933 3.743 -0.145 -0.1026 0.0518 0.0813 + 14OCO C1 40 0.437 4.389 3.238 0.3443 0.0273 -0.0594 + 14OCO C2 41 0.450 4.349 2.868 0.3252 0.0411 0.1307 + 14OCO PC 42 0.369 4.069 2.739 -0.1893 0.3512 -0.1832 + 15OCO C1 43 6.007 3.744 0.722 0.3071 0.3388 0.1801 + 15OCO C2 44 6.000 3.643 1.099 0.3063 -0.2992 -0.1867 + 15OCO PC 45 6.184 3.484 1.342 -0.1483 -0.5808 0.1744 + 16OCO C1 46 5.553 3.743 3.527 0.1026 0.3660 -0.4412 + 16OCO C2 47 5.311 3.423 3.477 -0.0022 0.1498 0.2565 + 16OCO PC 48 5.155 3.230 3.691 0.1222 0.1577 -0.0337 + 17OCO C1 49 4.769 1.705 4.290 -0.1774 -0.2782 -0.1356 + 17OCO C2 50 4.385 1.628 4.377 -0.2472 -0.0578 0.2482 + 17OCO PC 51 4.244 1.319 4.456 0.1680 -0.0527 -0.1492 + 18OCO C1 52 3.814 1.944 3.540 -0.2652 0.0032 -0.0650 + 18OCO C2 53 3.857 1.650 3.826 -0.2030 0.2660 0.0139 + 18OCO PC 54 3.831 1.425 4.102 0.1250 0.1795 -0.0372 + 19OCO C1 55 3.612 5.636 1.951 -0.0386 -0.0583 0.3415 + 19OCO C2 56 3.692 5.317 1.791 0.0504 0.0210 -0.0152 + 19OCO PC 57 3.572 5.086 1.604 0.0656 -0.0626 -0.3595 + 20OCO C1 58 1.014 1.487 2.938 0.2658 0.0481 -0.1053 + 20OCO C2 59 0.816 1.742 3.161 -0.0548 0.1243 -0.0890 + 20OCO PC 60 0.554 1.889 3.236 -0.0809 -0.2164 0.2358 + 21OCO C1 61 5.351 1.037 0.887 0.3410 0.2895 -0.1531 + 21OCO C2 62 5.555 1.075 1.224 -0.1400 -0.0562 -0.1655 + 21OCO PC 63 5.631 0.921 1.542 0.2101 -0.2110 -0.0376 + 22OCO C1 64 3.034 1.896 2.666 -0.0300 0.0203 0.1694 + 22OCO C2 65 3.445 1.973 2.659 0.0621 -0.0951 0.0733 + 22OCO PC 66 3.750 1.934 2.791 0.0273 -0.0691 -0.2565 + 23OCO C1 67 2.132 3.130 4.311 -0.4793 -0.0728 0.1492 + 23OCO C2 68 1.956 2.781 4.340 -0.0666 0.0074 0.1409 + 23OCO PC 69 1.757 2.575 4.185 -0.1284 0.3361 -0.0763 + 24OCO C1 70 0.865 2.766 1.567 0.2490 -0.2146 -0.1607 + 24OCO C2 71 0.596 2.982 1.378 -0.2869 0.2046 -0.5237 + 24OCO PC 72 0.494 3.279 1.240 -0.1821 0.5731 -0.1790 + 25OCO C1 73 1.535 5.354 1.353 0.2318 0.0871 -0.0704 + 25OCO C2 74 1.805 5.130 1.559 0.1892 -0.0181 0.0175 + 25OCO PC 75 2.126 5.211 1.725 -0.0454 -0.1236 -0.0739 + 26OCO C1 76 0.340 2.716 0.406 0.0112 -0.5354 -0.1271 + 26OCO C2 77 0.156 2.983 0.636 0.0264 0.4428 0.0371 + 26OCO PC 78 0.168 3.238 0.890 -0.3696 0.1895 -0.0774 + 27OCO C1 79 5.219 4.295 0.510 0.2191 -0.3355 0.3143 + 27OCO C2 80 5.363 4.107 0.210 -0.5263 -0.1094 -0.1180 + 27OCO PC 81 5.468 4.220 -0.110 -0.0445 0.1214 -0.2421 + 28OCO C1 82 4.113 4.947 1.260 -0.1323 0.1170 -0.2071 + 28OCO C2 83 4.267 4.760 1.006 -0.0849 0.0650 0.0072 + 28OCO PC 84 4.317 4.422 0.923 -0.4683 0.1831 0.0607 + 29OCO C1 85 3.962 2.086 3.951 -0.2705 -0.2158 -0.2353 + 29OCO C2 86 3.581 2.090 3.918 -0.1208 -0.2635 -0.0774 + 29OCO PC 87 3.347 1.926 3.828 -0.0612 0.1057 0.0480 + 30OCO C1 88 1.126 1.858 0.438 -0.0267 -0.0716 -0.3696 + 30OCO C2 89 0.939 1.708 0.167 -0.0506 0.0461 0.0846 + 30OCO PC 90 0.911 1.488 -0.118 0.0121 0.1414 -0.3273 + 31OCO C1 91 2.879 5.124 2.033 -0.0535 0.1041 0.1938 + 31OCO C2 92 2.536 5.329 2.237 -0.1934 -0.0512 0.1307 + 31OCO PC 93 2.309 5.197 2.460 0.1850 -0.4522 0.0465 + 32OCO C1 94 5.138 1.121 3.102 0.3028 -0.1075 0.1604 + 32OCO C2 95 5.443 1.380 3.150 -0.2277 0.1158 0.1116 + 32OCO PC 96 5.790 1.343 3.215 0.1009 -0.1241 0.2982 + 33OCO C1 97 2.428 4.960 3.655 -0.2118 -0.1392 -0.1727 + 33OCO C2 98 2.196 4.943 3.974 0.0222 -0.1979 0.3553 + 33OCO PC 99 1.873 4.991 3.947 -0.0881 -0.1072 -0.1763 + 34OCO C1 100 4.801 2.151 2.398 0.0383 -0.3302 -0.0224 + 34OCO C2 101 4.534 2.056 2.635 0.1714 0.1324 0.2429 + 34OCO PC 102 4.172 2.026 2.668 -0.4176 0.0412 -0.0366 + 35OCO C1 103 2.583 1.253 0.983 0.3509 0.1733 -0.1758 + 35OCO C2 104 2.415 1.613 0.988 -0.3826 0.2858 -0.3548 + 35OCO PC 105 2.384 1.911 1.047 -0.1891 0.3471 -0.1216 + 36OCO C1 106 2.278 1.815 4.546 -0.0501 0.0991 -0.0801 + 36OCO C2 107 1.900 1.938 4.414 -0.3711 -0.0529 -0.0692 + 36OCO PC 108 1.637 2.133 4.439 -0.1232 -0.1352 0.0416 + 37OCO C1 109 5.452 1.461 0.190 0.2052 0.1147 0.0845 + 37OCO C2 110 5.224 1.445 -0.090 -0.0855 -0.1956 -0.2546 + 37OCO PC 111 5.144 1.557 -0.416 -0.0187 0.1018 0.0483 + 38OCO C1 112 2.098 1.773 3.877 -0.5269 -0.0235 -0.0456 + 38OCO C2 113 2.130 1.360 3.904 0.2752 0.2519 0.4818 + 38OCO PC 114 2.129 1.086 4.124 0.1116 -0.1978 0.3713 + 39OCO C1 115 4.439 5.977 2.218 0.0962 -0.0432 -0.0894 + 39OCO C2 116 4.519 5.584 2.136 -0.0271 -0.0590 0.2259 + 39OCO PC 117 4.449 5.370 1.901 -0.1982 -0.1241 0.4338 + 40OCO C1 118 4.865 3.518 3.324 0.0581 0.0961 -0.2588 + 40OCO C2 119 4.769 3.281 3.033 0.0646 0.3648 -0.2472 + 40OCO PC 120 4.789 2.987 2.821 0.1502 0.1653 -0.1280 + 41OCO C1 121 3.672 1.376 1.203 0.0990 -0.1328 -0.2604 + 41OCO C2 122 3.692 1.069 1.490 -0.1937 -0.1746 -0.3184 + 41OCO PC 123 3.751 0.894 1.823 -0.0908 -0.1351 -0.0879 + 42OCO C1 124 1.146 2.368 1.575 0.2733 0.1325 0.1368 + 42OCO C2 125 1.131 2.233 1.230 0.2319 0.1165 0.1404 + 42OCO PC 126 1.138 2.416 0.937 0.2086 -0.0953 0.2385 + 43OCO C1 127 1.807 3.617 4.509 -0.0874 -0.2377 0.0449 + 43OCO C2 128 2.147 3.827 4.450 0.2630 -0.0676 0.3894 + 43OCO PC 129 2.404 4.034 4.483 -0.2243 -0.1199 -0.0455 + 44OCO C1 130 1.261 2.124 3.440 -0.0555 0.1631 -0.0406 + 44OCO C2 131 1.549 2.164 3.248 0.0909 -0.0568 0.2503 + 44OCO PC 132 1.731 2.094 3.000 -0.4792 -0.1253 0.4517 + 45OCO C1 133 5.519 3.088 3.148 -0.3964 0.2646 0.1212 + 45OCO C2 134 5.251 3.148 2.873 -0.4438 -0.3551 0.1323 + 45OCO PC 135 5.120 3.120 2.608 -0.1978 0.0455 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0.1349 0.2465 0.1673 + 589OCO PC 1767 0.713 3.802 2.656 0.2131 -0.0391 -0.1557 + 590OCO C1 1768 0.969 1.830 4.586 -0.4297 0.1893 0.0458 + 590OCO C2 1769 0.787 1.529 4.428 0.0828 -0.0729 -0.3074 + 590OCO PC 1770 0.797 1.199 4.234 -0.1926 -0.2964 -0.1409 + 591OCO C1 1771 1.368 3.491 3.299 0.0661 0.2395 0.5058 + 591OCO C2 1772 1.581 3.215 3.322 -0.0956 -0.2607 0.0344 + 591OCO PC 1773 1.569 2.899 3.436 -0.1140 0.0110 0.1962 + 592OCO C1 1774 0.601 4.114 0.888 -0.2497 -0.1670 0.0617 + 592OCO C2 1775 0.366 3.931 0.595 -0.0467 -0.2049 0.1198 + 592OCO PC 1776 0.383 3.943 0.265 0.0797 0.2418 0.3254 + 593OCO C1 1777 5.907 2.194 4.371 -0.0374 0.3065 0.3456 + 593OCO C2 1778 5.812 2.303 4.730 0.0924 -0.2215 -0.0023 + 593OCO PC 1779 5.976 2.359 5.046 0.0292 -0.1892 0.5755 + 594OCO C1 1780 1.875 5.985 1.648 0.3051 -0.3264 0.0418 + 594OCO C2 1781 1.519 5.883 1.566 0.2555 -0.1032 0.2267 + 594OCO PC 1782 1.256 5.764 1.317 0.0826 -0.0690 -0.0842 + 595OCO C1 1783 2.202 2.107 3.020 0.1721 0.2155 -0.2998 + 595OCO C2 1784 1.998 2.357 3.239 -0.1534 -0.1967 -0.1733 + 595OCO PC 1785 1.773 2.539 3.221 0.3215 0.0053 0.0074 + 596OCO C1 1786 5.574 5.718 4.759 -0.0465 -0.1869 -0.1237 + 596OCO C2 1787 5.740 5.752 5.117 -0.0621 -0.2528 -0.5423 + 596OCO PC 1788 5.746 5.729 5.512 -0.0373 -0.0412 0.1100 + 597OCO C1 1789 5.205 1.453 3.945 -0.4411 0.2522 0.0607 + 597OCO C2 1790 5.396 1.737 4.151 0.3029 0.0746 -0.1861 + 597OCO PC 1791 5.592 1.696 4.449 0.0503 -0.0161 -0.1144 + 598OCO C1 1792 3.811 1.008 3.887 -0.2145 0.2189 -0.4036 + 598OCO C2 1793 3.764 1.244 3.588 0.3212 0.3978 -0.1512 + 598OCO PC 1794 3.701 1.201 3.270 -0.1043 -0.0434 -0.2085 + 599OCO C1 1795 2.281 0.587 4.592 -0.0524 0.3403 0.0268 + 599OCO C2 1796 2.364 0.648 4.985 0.1449 -0.0197 0.1642 + 599OCO PC 1797 2.657 0.552 5.152 -0.2822 0.1967 0.0509 + 600OCO C1 1798 5.615 3.190 4.559 -0.1688 0.0384 0.0175 + 600OCO C2 1799 5.915 3.261 4.274 0.1764 -0.1377 -0.2509 + 600OCO PC 1800 5.884 3.466 3.939 -0.1512 -0.0020 -0.2203 + 601OCO C1 1801 4.106 0.450 0.590 -0.2106 -0.0699 0.0489 + 601OCO C2 1802 3.941 0.115 0.612 0.1034 -0.0485 -0.2097 + 601OCO PC 1803 3.723 -0.151 0.732 0.0141 -0.4209 0.2360 + 602OCO C1 1804 0.247 0.400 2.091 -0.2835 0.3840 -0.2069 + 602OCO C2 1805 0.367 0.579 1.785 0.1880 -0.2130 -0.3435 + 602OCO PC 1806 0.387 0.914 1.624 -0.1893 0.1379 -0.0876 + 603OCO C1 1807 3.233 3.061 1.357 -0.2791 0.0811 -0.2289 + 603OCO C2 1808 3.159 3.325 1.600 0.0020 0.0266 0.0866 + 603OCO PC 1809 3.126 3.657 1.697 -0.4800 0.3979 -0.3944 + 604OCO C1 1810 0.175 3.883 1.607 0.1432 0.2333 -0.1623 + 604OCO C2 1811 0.108 3.717 1.926 0.0174 0.1958 -0.1480 + 604OCO PC 1812 0.233 3.456 2.142 0.0049 -0.0343 -0.3929 + 605OCO C1 1813 3.133 0.302 2.370 -0.0434 0.0671 -0.0625 + 605OCO C2 1814 2.910 0.035 2.464 -0.1673 0.2433 0.2107 + 605OCO PC 1815 2.745 -0.192 2.714 -0.3189 -0.3825 -0.1401 + 606OCO C1 1816 3.363 3.627 3.438 0.1292 -0.1768 0.1565 + 606OCO C2 1817 3.466 3.324 3.182 -0.2603 -0.0944 0.0822 + 606OCO PC 1818 3.369 3.295 2.822 -0.0599 -0.2365 0.0699 + 607OCO C1 1819 3.850 5.458 3.298 0.0733 -0.0308 -0.3169 + 607OCO C2 1820 4.059 5.376 3.614 0.2667 -0.2939 -0.1927 + 607OCO PC 1821 4.064 5.528 3.960 -0.1309 -0.3442 0.0256 + 608OCO C1 1822 5.207 4.852 0.400 -0.3217 -0.1718 -0.0288 + 608OCO C2 1823 5.525 4.708 0.573 0.0909 -0.0897 -0.1979 + 608OCO PC 1824 5.746 4.696 0.832 0.1285 0.1156 -0.1138 + 609OCO C1 1825 2.231 2.503 4.581 -0.0838 -0.0833 0.1394 + 609OCO C2 1826 2.553 2.299 4.529 0.2635 0.1259 -0.0989 + 609OCO PC 1827 2.903 2.365 4.576 0.0601 -0.0828 0.0798 + 610OCO C1 1828 1.383 0.749 2.122 0.0970 0.0665 0.1671 + 610OCO C2 1829 1.685 0.483 2.236 -0.1230 0.0865 0.0328 + 610OCO PC 1830 2.023 0.478 2.328 0.3113 -0.1125 0.0651 + 611OCO C1 1831 0.658 4.036 2.155 -0.0351 -0.3929 -0.0445 + 611OCO C2 1832 0.536 3.732 1.954 0.0317 0.2725 -0.1103 + 611OCO PC 1833 0.606 3.546 1.675 -0.0251 0.0886 0.1123 + 612OCO C1 1834 0.183 6.053 2.420 0.0967 -0.0122 0.0925 + 612OCO C2 1835 0.527 6.080 2.526 0.1820 0.0547 -0.0041 + 612OCO PC 1836 0.825 5.890 2.563 -0.0337 0.2922 0.0795 + 613OCO C1 1837 1.887 1.293 0.096 0.0426 0.4001 -0.0125 + 613OCO C2 1838 1.637 1.553 0.073 0.1044 -0.1037 -0.0044 + 613OCO PC 1839 1.369 1.816 0.061 -0.3580 0.2259 0.1325 + 614OCO C1 1840 4.674 1.675 1.579 -0.3017 -0.0020 0.3863 + 614OCO C2 1841 4.412 1.896 1.761 0.2080 -0.4611 -0.0934 + 614OCO PC 1842 4.076 1.930 1.859 -0.6157 -0.2202 0.1326 + 615OCO C1 1843 0.147 5.988 0.202 -0.0768 -0.3833 -0.2296 + 615OCO C2 1844 0.055 5.909 -0.169 -0.0777 -0.0035 0.1428 + 615OCO PC 1845 0.220 5.968 -0.478 0.2196 0.2705 -0.3132 + 616OCO C1 1846 1.181 5.659 2.268 -0.0351 0.2710 -0.2370 + 616OCO C2 1847 0.843 5.546 2.252 0.0735 -0.0215 -0.1603 + 616OCO PC 1848 0.563 5.636 2.190 0.1840 -0.1924 -0.3569 + 617OCO C1 1849 2.689 0.567 3.929 -0.0080 -0.0570 0.0702 + 617OCO C2 1850 2.445 0.416 3.676 -0.2916 -0.1887 -0.3718 + 617OCO PC 1851 2.147 0.220 3.706 0.0649 0.1965 -0.1249 + 618OCO C1 1852 3.732 2.715 1.413 -0.1693 0.0137 -0.0392 + 618OCO C2 1853 3.807 2.988 1.661 -0.2187 -0.2369 -0.0455 + 618OCO PC 1854 4.002 3.208 1.788 0.2405 0.0784 -0.3015 + 619OCO C1 1855 4.598 5.360 2.637 0.4670 -0.0696 -0.5133 + 619OCO C2 1856 4.510 5.707 2.646 0.4601 -0.3816 -0.0436 + 619OCO PC 1857 4.469 6.024 2.794 0.2115 0.1712 -0.1311 + 620OCO C1 1858 5.850 0.711 4.083 -0.0698 0.2036 -0.1769 + 620OCO C2 1859 5.736 0.390 3.844 -0.2377 -0.0532 -0.2271 + 620OCO PC 1860 5.515 0.222 3.806 -0.0721 -0.0614 0.0884 + 621OCO C1 1861 4.639 4.068 1.997 -0.1039 0.2344 -0.0110 + 621OCO C2 1862 5.039 3.984 1.985 0.3374 0.1979 -0.2423 + 621OCO PC 1863 5.377 3.918 1.909 0.2487 0.0360 -0.1521 + 622OCO C1 1864 5.542 1.217 1.906 0.0144 -0.0087 0.0847 + 622OCO C2 1865 5.155 1.124 1.950 0.1062 0.2356 0.1402 + 622OCO PC 1866 4.835 1.136 2.121 0.0344 -0.1879 0.0613 + 623OCO C1 1867 3.716 5.983 1.715 0.0557 0.1420 0.2181 + 623OCO C2 1868 3.637 6.142 1.431 -0.1261 0.0505 0.5023 + 623OCO PC 1869 3.702 6.211 1.119 0.2156 -0.0347 0.0907 + 624OCO C1 1870 1.544 2.898 3.006 0.1302 0.3894 -0.1513 + 624OCO C2 1871 1.329 2.640 3.108 -0.0829 -0.0665 0.2077 + 624OCO PC 1872 1.161 2.395 2.930 -0.2042 0.2367 -0.2301 + 625OCO C1 1873 2.678 2.449 2.238 0.0378 0.2144 -0.1258 + 625OCO C2 1874 2.765 2.319 1.857 -0.0389 -0.4392 0.3967 + 625OCO PC 1875 2.698 2.248 1.508 -0.1480 0.3622 -0.0546 + 626OCO C1 1876 3.824 1.714 1.471 -0.2385 -0.1652 0.2844 + 626OCO C2 1877 4.018 1.483 1.717 -0.0281 0.7202 0.3535 + 626OCO PC 1878 4.247 1.404 1.924 -0.4596 -0.4789 -0.0866 + 627OCO C1 1879 2.535 1.733 0.460 0.2360 -0.2532 0.0740 + 627OCO C2 1880 2.713 1.833 0.159 -0.0106 0.2323 -0.2354 + 627OCO PC 1881 2.698 2.004 -0.193 -0.0400 -0.1336 0.0113 + 628OCO C1 1882 0.084 3.728 2.898 0.0872 0.1124 -0.3398 + 628OCO C2 1883 0.300 3.442 2.829 -0.1465 0.0030 -0.0264 + 628OCO PC 1884 0.553 3.248 2.861 -0.2957 -0.0848 0.2929 + 629OCO C1 1885 4.254 2.079 3.604 -0.0618 0.2798 -0.0081 + 629OCO C2 1886 4.222 1.887 3.237 -0.3191 0.1116 -0.0031 + 629OCO PC 1887 4.344 1.792 2.958 -0.2241 -0.3798 0.0062 + 630OCO C1 1888 1.883 0.706 4.551 -0.0012 -0.2955 0.0406 + 630OCO C2 1889 2.107 1.003 4.692 0.1170 -0.1788 0.0406 + 630OCO PC 1890 2.333 1.269 4.618 -0.1707 -0.3077 -0.4035 + 631OCO C1 1891 0.448 2.888 2.882 -0.1560 0.2137 0.0174 + 631OCO C2 1892 0.597 2.887 2.508 0.1408 0.0843 -0.1083 + 631OCO PC 1893 0.596 2.946 2.157 0.0927 0.1820 0.2524 + 632OCO C1 1894 5.297 3.376 0.342 0.1670 0.1772 -0.3525 + 632OCO C2 1895 5.259 3.706 0.196 0.0385 0.1480 -0.1334 + 632OCO PC 1896 5.116 3.892 -0.015 -0.1375 -0.4096 -0.3597 + 633OCO C1 1897 5.468 5.290 4.202 0.1304 0.1839 0.4192 + 633OCO C2 1898 5.462 5.144 4.525 -0.2474 0.0660 0.2611 + 633OCO PC 1899 5.696 5.130 4.762 -0.3157 0.0766 0.0778 + 634OCO C1 1900 1.752 0.004 1.178 -0.0338 0.1290 0.3246 + 634OCO C2 1901 2.032 -0.173 1.058 0.0344 0.1682 -0.0327 + 634OCO PC 1902 2.228 -0.409 0.933 0.3585 -0.1960 -0.3771 + 635OCO C1 1903 3.740 2.579 0.958 0.0025 0.0921 0.2329 + 635OCO C2 1904 4.032 2.716 0.681 0.0528 -0.0538 0.1401 + 635OCO PC 1905 4.319 2.880 0.613 -0.0156 -0.1328 0.1682 + 636OCO C1 1906 1.899 3.042 2.663 -0.1354 -0.3106 0.2204 + 636OCO C2 1907 2.271 3.040 2.662 -0.2131 0.3004 -0.3580 + 636OCO PC 1908 2.593 2.908 2.788 0.1823 0.6048 0.2145 + 637OCO C1 1909 0.576 3.482 3.909 0.2366 0.0291 -0.2532 + 637OCO C2 1910 0.681 3.143 3.844 -0.1084 0.3140 -0.1667 + 637OCO PC 1911 0.500 2.829 3.984 -0.0032 -0.4873 -0.1600 + 638OCO C1 1912 2.825 0.998 3.907 0.1330 -0.0463 -0.0263 + 638OCO C2 1913 2.444 0.950 3.869 0.1198 0.4128 0.1152 + 638OCO PC 1914 2.135 1.010 3.690 -0.1391 -0.0051 0.0375 + 639OCO C1 1915 2.673 0.010 2.043 0.2981 0.1649 0.0312 + 639OCO C2 1916 2.408 -0.084 1.845 -0.0135 0.2087 -0.1413 + 639OCO PC 1917 2.368 -0.177 1.548 -0.4519 0.0097 -0.1693 + 640OCO C1 1918 0.977 5.922 4.975 0.0898 0.1339 -0.0780 + 640OCO C2 1919 1.243 5.718 4.892 0.0569 0.2476 0.0038 + 640OCO PC 1920 1.441 5.526 4.776 0.2652 0.0680 -0.1601 + 641OCO C1 1921 1.254 1.322 3.736 0.0375 0.4445 -0.1111 + 641OCO C2 1922 1.166 1.029 3.889 0.1845 0.0339 0.0486 + 641OCO PC 1923 0.995 0.749 3.895 -0.2744 0.0718 0.2911 + 642OCO C1 1924 2.831 1.228 1.501 0.0795 -0.0773 -0.1757 + 642OCO C2 1925 2.689 1.488 1.304 0.2491 0.0419 -0.1158 + 642OCO PC 1926 2.752 1.794 1.272 0.0738 0.1094 -0.1406 + 643OCO C1 1927 3.213 3.604 1.225 -0.2191 0.1647 -0.0471 + 643OCO C2 1928 3.483 3.755 1.504 0.1369 -0.1827 0.3542 + 643OCO PC 1929 3.771 3.626 1.600 0.1332 -0.1510 0.0840 + 644OCO C1 1930 3.484 0.906 3.491 -0.0986 0.1880 -0.0798 + 644OCO C2 1931 3.209 1.129 3.452 -0.1032 0.0490 -0.0929 + 644OCO PC 1932 3.030 1.396 3.315 0.0958 -0.2697 -0.1445 + 645OCO C1 1933 3.460 0.392 1.894 -0.0556 -0.1050 0.0933 + 645OCO C2 1934 3.556 0.369 2.248 0.0781 -0.0614 -0.0191 + 645OCO PC 1935 3.597 0.170 2.531 0.2794 0.1199 0.2251 + 646OCO C1 1936 4.225 2.005 1.299 0.2231 0.0492 -0.0504 + 646OCO C2 1937 3.982 1.849 1.051 0.4549 0.1461 -0.1413 + 646OCO PC 1938 3.827 1.592 0.896 0.2101 -0.1475 0.2834 + 647OCO C1 1939 5.899 2.771 5.018 0.3420 -0.0765 0.4185 + 647OCO C2 1940 5.653 2.888 5.326 -0.1684 -0.3364 -0.3619 + 647OCO PC 1941 5.389 3.006 5.562 0.2258 0.2373 0.0829 + 648OCO C1 1942 3.344 4.606 0.269 -0.2041 0.1403 0.0759 + 648OCO C2 1943 3.399 5.017 0.167 0.2521 0.2252 -0.0311 + 648OCO PC 1944 3.360 5.318 0.010 0.2042 0.1221 -0.1595 + 649OCO C1 1945 0.438 6.015 0.798 -0.0239 -0.0254 -0.0709 + 649OCO C2 1946 0.353 6.267 0.495 -0.0407 0.0497 0.1002 + 649OCO PC 1947 0.318 6.519 0.285 0.5196 -0.0961 -0.0675 + 650OCO C1 1948 5.858 3.593 2.176 -0.3602 0.1016 0.0034 + 650OCO C2 1949 5.708 3.516 2.452 0.2294 -0.0004 0.2267 + 650OCO PC 1950 5.389 3.479 2.614 0.1082 0.1376 0.2008 + 651OCO C1 1951 0.689 2.544 1.222 0.1856 -0.2790 -0.2932 + 651OCO C2 1952 0.679 2.187 1.032 -0.1026 0.2856 -0.0714 + 651OCO PC 1953 0.883 1.979 0.922 -0.0468 -0.1382 0.0797 + 652OCO C1 1954 4.847 2.080 1.541 -0.3233 0.0151 0.0187 + 652OCO C2 1955 5.166 2.199 1.357 0.0279 0.2449 0.4768 + 652OCO PC 1956 5.370 2.247 1.038 -0.2353 -0.2137 0.2345 + 653OCO C1 1957 2.275 1.545 3.505 0.1616 0.2493 0.2801 + 653OCO C2 1958 2.026 1.782 3.428 0.2481 0.1632 0.0769 + 653OCO PC 1959 1.859 2.069 3.525 -0.1051 -0.0300 -0.3468 + 654OCO C1 1960 3.872 1.863 4.865 0.0976 0.1243 0.2883 + 654OCO C2 1961 3.504 1.821 4.678 -0.1145 -0.3719 0.1199 + 654OCO PC 1962 3.382 1.850 4.323 0.0551 -0.0879 0.1094 + 655OCO C1 1963 3.187 4.679 0.724 0.0370 0.4245 0.0371 + 655OCO C2 1964 3.484 4.698 0.946 0.2777 -0.1937 0.0241 + 655OCO PC 1965 3.821 4.712 0.990 0.1684 -0.1383 0.1539 + 656OCO C1 1966 4.453 3.860 0.481 -0.0679 0.5613 0.2950 + 656OCO C2 1967 4.374 3.986 0.114 0.1025 -0.3696 0.3156 + 656OCO PC 1968 4.515 4.085 -0.190 0.1563 -0.5886 -0.1334 + 657OCO C1 1969 0.588 6.042 2.074 -0.2063 0.0093 -0.1117 + 657OCO C2 1970 0.962 5.855 1.933 0.3292 0.3589 -0.0229 + 657OCO PC 1971 1.221 5.703 1.802 0.0985 0.5722 0.0781 + 658OCO C1 1972 5.427 0.076 4.547 0.1815 -0.1926 0.1449 + 658OCO C2 1973 5.604 0.274 4.887 -0.1583 0.2846 0.3528 + 658OCO PC 1974 5.528 0.544 5.096 0.0313 -0.0583 0.1574 + 659OCO C1 1975 3.289 1.005 4.083 -0.3437 -0.3948 -0.0491 + 659OCO C2 1976 3.168 0.672 4.193 -0.1873 -0.1593 -0.2062 + 659OCO PC 1977 3.259 0.342 4.187 -0.0548 0.2154 -0.1969 + 660OCO C1 1978 4.552 1.244 3.216 -0.0622 0.1826 0.0283 + 660OCO C2 1979 4.194 1.156 3.090 0.3649 0.2386 0.2855 + 660OCO PC 1980 4.119 1.083 2.713 0.3361 0.2103 0.0656 + 661OCO C1 1981 0.628 4.796 0.674 -0.1014 0.0231 0.0176 + 661OCO C2 1982 1.003 4.935 0.729 0.1040 0.2552 0.4082 + 661OCO PC 1983 1.328 4.779 0.739 -0.1573 -0.1291 -0.2617 + 662OCO C1 1984 5.057 0.132 3.996 -0.2582 0.1184 -0.0481 + 662OCO C2 1985 4.761 0.317 4.095 -0.1759 -0.3661 -0.0703 + 662OCO PC 1986 4.426 0.358 4.064 0.0862 -0.1464 0.1312 + 663OCO C1 1987 0.443 4.275 4.858 0.2431 -0.0967 -0.2740 + 663OCO C2 1988 0.699 4.012 4.802 0.1656 0.1555 -0.1501 + 663OCO PC 1989 1.014 3.941 4.627 0.0375 -0.3171 0.0182 + 664OCO C1 1990 2.136 2.994 1.716 0.2555 -0.0834 0.0408 + 664OCO C2 1991 2.190 2.609 1.843 0.0802 -0.3618 -0.0874 + 664OCO PC 1992 2.232 2.450 2.174 -0.0936 -0.3080 -0.0535 + 665OCO C1 1993 3.290 4.091 4.672 -0.3253 -0.1153 -0.3519 + 665OCO C2 1994 3.016 3.871 4.554 -0.1596 0.0433 0.1014 + 665OCO PC 1995 2.742 3.827 4.728 0.4540 0.3118 0.2468 + 666OCO C1 1996 0.971 5.613 4.310 0.3198 -0.0890 0.0490 + 666OCO C2 1997 0.802 5.612 4.654 0.4047 -0.0168 -0.0967 + 666OCO PC 1998 0.675 5.438 4.972 0.0476 -0.0605 0.0040 + 667OCO C1 1999 1.365 3.245 4.278 -0.1285 -0.0658 0.1704 + 667OCO C2 2000 1.430 2.896 4.179 0.0677 -0.0349 -0.7275 + 667OCO PC 2001 1.352 2.631 3.991 0.0975 0.1052 -0.2146 + 668OCO C1 2002 1.740 3.973 1.120 -0.2775 -0.0938 -0.0536 + 668OCO C2 2003 2.068 3.824 1.049 0.0269 0.1024 -0.0705 + 668OCO PC 2004 2.391 3.740 1.137 0.1898 0.0744 0.0988 + 669OCO C1 2005 1.389 1.150 0.963 -0.2419 0.1632 0.0643 + 669OCO C2 2006 1.254 1.417 1.184 0.0520 -0.0784 0.0051 + 669OCO PC 2007 1.185 1.461 1.502 -0.0623 -0.0425 0.6436 + 670OCO C1 2008 2.075 3.107 3.432 0.1242 -0.5803 -0.0983 + 670OCO C2 2009 2.005 3.276 3.109 -0.3165 0.3369 0.1761 + 670OCO PC 2010 2.046 3.424 2.778 0.0429 0.0629 -0.1372 + 671OCO C1 2011 1.251 3.965 3.351 -0.1072 -0.0201 0.1911 + 671OCO C2 2012 1.278 3.673 3.672 0.2313 0.2310 0.4657 + 671OCO PC 2013 1.256 3.575 3.998 -0.4343 -0.0349 -0.1039 + 672OCO C1 2014 5.831 0.190 1.132 0.1663 0.1726 0.0169 + 672OCO C2 2015 5.815 0.607 1.041 0.0496 0.0788 0.0327 + 672OCO PC 2016 5.808 0.807 0.741 -0.1322 0.1031 -0.0130 + 673OCO C1 2017 0.061 2.600 3.184 -0.1392 0.4494 0.3516 + 673OCO C2 2018 -0.142 2.380 2.922 -0.3927 -0.0728 -0.0742 + 673OCO PC 2019 -0.408 2.300 2.811 0.0403 -0.2082 0.2249 + 674OCO C1 2020 5.887 0.984 2.659 -0.1387 -0.1261 0.1576 + 674OCO C2 2021 6.006 0.863 2.995 -0.2194 0.1187 -0.0553 + 674OCO PC 2022 6.275 0.790 3.182 0.1191 0.2799 -0.2254 + 675OCO C1 2023 2.345 2.908 4.566 0.3727 -0.0657 -0.1279 + 675OCO C2 2024 2.387 3.019 4.949 0.0566 -0.1178 -0.0112 + 675OCO PC 2025 2.581 3.233 5.171 0.0065 0.0749 0.0785 + 676OCO C1 2026 1.651 1.392 3.954 -0.1992 0.1421 -0.2790 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2044 2.571 3.222 3.066 0.3806 0.0286 0.1132 + 682OCO C2 2045 2.383 3.557 3.086 -0.0389 0.2520 -0.0506 + 682OCO PC 2046 2.230 3.868 3.162 -0.1177 -0.1710 -0.2360 + 683OCO C1 2047 4.324 4.485 0.001 -0.3261 -0.0635 0.1780 + 683OCO C2 2048 4.281 4.829 0.195 -0.2110 0.0692 0.2827 + 683OCO PC 2049 4.401 5.174 0.230 -0.2177 -0.2034 0.0604 + 684OCO C1 2050 1.280 2.363 0.469 -0.0706 0.2975 -0.3061 + 684OCO C2 2051 1.482 2.534 0.739 -0.2754 0.0160 -0.5683 + 684OCO PC 2052 1.487 2.700 1.061 0.0692 0.3279 -0.1101 + 685OCO C1 2053 5.326 0.597 0.807 -0.0943 0.0545 -0.0076 + 685OCO C2 2054 4.917 0.511 0.909 -0.1389 0.0244 -0.0691 + 685OCO PC 2055 4.600 0.421 0.972 0.0569 0.2001 0.0166 + 686OCO C1 2056 3.247 1.442 1.034 -0.1235 0.0172 0.1618 + 686OCO C2 2057 3.438 1.535 0.722 0.2262 0.3668 -0.2004 + 686OCO PC 2058 3.629 1.641 0.515 0.2400 -0.1899 0.1828 + 687OCO C1 2059 1.000 0.268 0.260 -0.1195 -0.1559 0.0360 + 687OCO C2 2060 1.309 0.110 0.036 0.0991 0.1629 -0.1019 + 687OCO PC 2061 1.576 -0.122 -0.090 -0.2555 0.3071 -0.0004 + 688OCO C1 2062 0.395 1.304 3.455 0.0471 0.1993 -0.1274 + 688OCO C2 2063 0.478 1.641 3.593 0.0738 -0.2018 0.0579 + 688OCO PC 2064 0.695 1.913 3.657 0.2891 -0.0267 0.1422 + 689OCO C1 2065 1.597 4.681 2.708 -0.1210 0.1705 0.0940 + 689OCO C2 2066 1.439 4.859 3.047 -0.2003 -0.2345 0.0575 + 689OCO PC 2067 1.332 4.972 3.332 -0.0668 0.3261 -0.0103 + 690OCO C1 2068 5.528 2.894 0.971 -0.2299 0.1824 0.2204 + 690OCO C2 2069 5.763 2.713 1.169 0.0616 0.1678 -0.0721 + 690OCO PC 2070 5.946 2.689 1.486 -0.0527 -0.0885 -0.3474 + 691OCO C1 2071 3.932 3.830 1.225 0.1051 0.3252 0.0403 + 691OCO C2 2072 4.076 4.171 1.257 -0.2598 0.1424 -0.1389 + 691OCO PC 2073 4.065 4.548 1.308 -0.0331 0.0485 -0.3678 + 692OCO C1 2074 2.005 1.441 2.694 -0.0460 -0.2180 0.2662 + 692OCO C2 2075 2.145 1.107 2.509 0.1375 -0.3745 -0.1784 + 692OCO PC 2076 2.283 0.813 2.497 -0.0538 0.3291 -0.1533 + 693OCO C1 2077 3.870 4.490 3.454 -0.1644 -0.1639 0.2630 + 693OCO C2 2078 3.763 4.391 3.110 0.1250 0.2493 0.1325 + 693OCO PC 2079 3.572 4.528 2.918 -0.2313 0.3598 0.3553 + 694OCO C1 2080 5.038 2.576 1.797 -0.1790 -0.3132 0.0888 + 694OCO C2 2081 5.229 2.209 1.801 0.1020 -0.6238 -0.1100 + 694OCO PC 2082 5.517 2.034 1.884 0.0037 0.4258 -0.0593 + 695OCO C1 2083 3.329 0.851 1.672 0.4779 -0.0048 -0.0495 + 695OCO C2 2084 3.130 0.648 1.442 -0.0643 -0.0413 0.3434 + 695OCO PC 2085 2.797 0.507 1.459 0.0268 0.0794 0.1513 + 696OCO C1 2086 5.958 2.408 2.487 0.1637 -0.0726 -0.4591 + 696OCO C2 2087 6.211 2.256 2.231 0.1436 0.0449 -0.1531 + 696OCO PC 2088 6.394 2.115 1.971 -0.0210 0.0449 0.0505 + 697OCO C1 2089 4.065 2.979 2.291 0.0784 0.4078 -0.2165 + 697OCO C2 2090 4.190 3.323 2.322 0.3035 -0.0583 0.0332 + 697OCO PC 2091 4.452 3.538 2.168 0.0760 -0.0126 -0.1672 + 698OCO C1 2092 4.343 4.914 4.170 -0.1523 -0.0247 -0.0523 + 698OCO C2 2093 4.350 4.728 4.463 -0.1464 0.0646 -0.1513 + 698OCO PC 2094 4.262 4.406 4.473 -0.1659 0.1753 0.0905 + 699OCO C1 2095 0.508 0.511 0.735 0.3380 -0.0233 -0.3576 + 699OCO C2 2096 0.800 0.661 0.643 -0.1145 0.3526 0.1034 + 699OCO PC 2097 0.917 0.901 0.495 -0.2404 -0.3276 -0.1432 + 700OCO C1 2098 3.601 5.062 2.719 0.2919 -0.0161 0.0400 + 700OCO C2 2099 3.219 5.126 2.885 -0.0483 0.0324 0.1750 + 700OCO PC 2100 2.949 5.078 3.075 0.0840 0.2768 -0.1746 + 701OCO C1 2101 3.586 3.322 1.380 -0.0325 -0.1342 -0.0620 + 701OCO C2 2102 3.537 3.276 1.007 -0.0929 -0.2476 -0.0618 + 701OCO PC 2103 3.331 3.424 0.789 -0.3737 0.3055 -0.0561 + 702OCO C1 2104 5.078 2.113 2.754 0.2990 -0.7366 0.2770 + 702OCO C2 2105 5.036 2.206 3.099 -0.2535 -0.1100 0.1268 + 702OCO PC 2106 4.957 2.471 3.333 -0.0945 -0.0773 -0.1624 + 703OCO C1 2107 2.906 4.535 2.064 -0.2603 -0.1647 0.0813 + 703OCO C2 2108 2.740 4.219 2.223 0.1178 0.0019 -0.0289 + 703OCO PC 2109 2.876 3.985 2.403 -0.2469 -0.1447 0.1650 + 704OCO C1 2110 0.353 0.039 1.636 0.0311 0.1167 0.1335 + 704OCO C2 2111 -0.012 0.049 1.590 0.0873 -0.4857 -0.0015 + 704OCO PC 2112 -0.325 0.022 1.628 0.3480 0.2747 0.1741 + 705OCO C1 2113 1.500 0.880 2.587 0.2324 -0.4618 0.1863 + 705OCO C2 2114 1.790 0.904 2.391 -0.0655 0.1927 0.0469 + 705OCO PC 2115 2.011 0.912 2.136 -0.1331 0.2476 0.1838 + 706OCO C1 2116 3.637 3.707 2.933 -0.1889 -0.2160 0.4267 + 706OCO C2 2117 3.955 3.864 2.792 -0.3707 0.0135 0.0034 + 706OCO PC 2118 4.187 4.049 2.939 0.1552 -0.3154 0.0045 + 707OCO C1 2119 2.752 3.049 2.392 0.0633 -0.2162 0.1718 + 707OCO C2 2120 3.126 2.906 2.407 0.0729 0.1725 -0.1160 + 707OCO PC 2121 3.425 2.838 2.554 0.3391 0.0349 -0.1953 + 708OCO C1 2122 0.140 2.003 3.019 0.1393 0.0192 0.0903 + 708OCO C2 2123 0.239 1.654 3.002 -0.1431 -0.0444 -0.0334 + 708OCO PC 2124 0.545 1.498 2.850 -0.2075 0.0695 0.0640 + 709OCO C1 2125 1.855 5.026 3.118 0.1312 0.0452 -0.1374 + 709OCO C2 2126 2.193 5.213 3.176 0.4087 -0.2310 -0.4034 + 709OCO PC 2127 2.431 5.398 3.043 0.3734 -0.2689 0.0659 + 710OCO C1 2128 0.986 4.299 0.732 0.0515 0.1281 0.0296 + 710OCO C2 2129 1.335 4.345 0.821 -0.0503 0.1072 -0.5185 + 710OCO PC 2130 1.607 4.420 0.728 0.1130 0.2315 0.4815 + 711OCO C1 2131 3.803 3.718 0.119 -0.2745 -0.0127 0.2363 + 711OCO C2 2132 3.733 3.731 -0.284 -0.0051 0.2791 0.0299 + 711OCO PC 2133 3.571 3.857 -0.539 -0.4012 0.0714 0.2427 + 712OCO C1 2134 4.924 0.798 0.537 -0.2035 0.2126 0.1235 + 712OCO C2 2135 4.907 0.684 0.172 -0.0318 -0.0805 -0.1369 + 712OCO PC 2136 4.775 0.743 -0.130 0.1711 0.1977 -0.0931 + 713OCO C1 2137 0.340 2.275 3.273 -0.1512 0.6275 -0.1982 + 713OCO C2 2138 0.047 2.271 3.437 0.2143 0.1049 -0.2282 + 713OCO PC 2139 -0.309 2.234 3.398 0.0084 -0.3583 -0.0224 + 714OCO C1 2140 4.824 3.349 0.938 -0.0511 -0.1055 -0.0695 + 714OCO C2 2141 4.715 3.121 1.240 -0.0212 -0.1854 0.0109 + 714OCO PC 2142 4.811 2.980 1.542 -0.2774 0.0526 0.1127 + 715OCO C1 2143 1.794 5.413 0.663 -0.1989 -0.0231 0.1592 + 715OCO C2 2144 1.968 5.335 1.021 0.1487 -0.3130 -0.0577 + 715OCO PC 2145 2.050 5.483 1.350 -0.3285 -0.3516 -0.2291 + 716OCO C1 2146 2.105 1.433 1.278 0.3707 0.0761 -0.0083 + 716OCO C2 2147 2.325 1.737 1.433 -0.4232 -0.4229 0.0131 + 716OCO PC 2148 2.552 1.861 1.705 0.0406 0.0568 0.1210 + 717OCO C1 2149 0.616 0.388 2.399 0.0914 0.0226 0.4032 + 717OCO C2 2150 0.991 0.272 2.326 -0.2159 -0.2695 0.0977 + 717OCO PC 2151 1.341 0.166 2.269 0.4139 0.1536 -0.3698 + 718OCO C1 2152 3.551 0.716 2.600 -0.0369 0.0720 0.0242 + 718OCO C2 2153 3.171 0.670 2.674 0.0467 0.2682 0.1292 + 718OCO PC 2154 2.978 0.396 2.766 -0.3388 0.1702 0.1055 + 719OCO C1 2155 5.538 5.352 3.756 -0.0001 0.2871 0.2376 + 719OCO C2 2156 5.920 5.311 3.740 0.1790 -0.1238 0.2734 + 719OCO PC 2157 6.211 5.179 3.877 -0.2611 0.5927 -0.0694 + 720OCO C1 2158 3.791 2.188 0.128 -0.1193 0.3966 0.0244 + 720OCO C2 2159 3.976 1.969 0.400 0.2012 0.1652 0.2413 + 720OCO PC 2160 4.119 1.752 0.639 -0.4702 -0.2873 0.1808 + 721OCO C1 2161 6.001 4.568 1.159 0.2551 -0.0361 -0.2775 + 721OCO C2 2162 5.750 4.585 1.458 -0.2066 -0.0983 0.3974 + 721OCO PC 2163 5.440 4.620 1.575 0.2084 -0.0827 -0.3394 + 722OCO C1 2164 2.848 1.582 2.965 -0.0337 0.3519 0.2617 + 722OCO C2 2165 2.613 1.354 3.174 0.0666 0.6764 -0.0787 + 722OCO PC 2166 2.486 1.150 3.392 -0.0292 0.0646 -0.0595 + 723OCO C1 2167 3.112 4.201 0.475 -0.1394 -0.2141 -0.1373 + 723OCO C2 2168 3.407 4.353 0.659 0.3281 0.1712 0.3006 + 723OCO PC 2169 3.704 4.475 0.619 0.0924 0.0065 -0.2186 + 724OCO C1 2170 4.249 5.559 3.162 0.1245 0.2650 0.2993 + 724OCO C2 2171 4.024 5.901 3.057 -0.1231 0.4420 0.1332 + 724OCO PC 2172 3.848 6.174 2.860 -0.3592 0.1527 0.1516 + 725OCO C1 2173 4.244 1.738 3.975 -0.1932 0.2123 -0.2318 + 725OCO C2 2174 4.616 1.649 3.901 -0.1971 -0.4333 -0.1056 + 725OCO PC 2175 4.918 1.810 3.923 -0.0089 0.4591 -0.0464 + 726OCO C1 2176 4.481 2.587 3.473 0.2196 -0.2412 0.2739 + 726OCO C2 2177 4.167 2.505 3.693 -0.0852 -0.1971 0.4765 + 726OCO PC 2178 3.895 2.530 3.872 -0.1497 0.4744 0.2259 + 727OCO C1 2179 0.814 5.137 0.239 -0.0479 0.2287 -0.2091 + 727OCO C2 2180 0.558 4.829 0.217 0.0226 -0.1076 -0.3571 + 727OCO PC 2181 0.468 4.471 0.184 -0.2104 -0.0574 -0.3108 + 728OCO C1 2182 4.682 2.148 3.631 -0.2949 0.1720 -0.0737 + 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b/doc/examples/martini/run.mdp new file mode 100644 index 00000000..88e034e6 --- /dev/null +++ b/doc/examples/martini/run.mdp @@ -0,0 +1,108 @@ +include = +integrator = sd +; start time and timestep in ps = +tinit = 0 +dt = 0.020 + +nsteps = 200000 + +; We remove center of mass motion. In periodic boundary conditions, the center of mass motion is spurious; the periodic system is the same in all translational directions. +comm-mode = Linear +; number of steps for center of mass motion removal = +nstcomm = 10 + +nstxout = 0 +nstvout = 0 +nstfout = 0 +; Output frequency for energies to log file and energy file +nstlog = 500 +nstenergy = 200 +nstcalcenergy = 10 +; Output frequency and precisi500on for xtc file +nstxtcout = 250 +xtc-precision = 1000 + +cutoff-scheme = Verlet +nstlist = 20 +;rlist = 1.2 + +coulombtype = cutoff +coulomb-modifier = Potential-shift-verlet +rcoulomb = 1.1 +epsilon_r = 15 ; 2.5 (with polarizable water) +vdw_type = cutoff +vdw-modifier = Potential-shift-verlet +rvdw = 1.1 + +;coulombtype = Shift +;rcoulomb_switch = 0.0 +;rcoulomb = 1.2 +;epsilon_r = 15 +;vdw_type = Shift +;rvdw_switch = 0.9 +;rvdw = 1.2 + + +gen-vel = yes +gen-temp = 300 +gen_seed = 175547 +tc-grps = System +tcoupl = v-rescale +tau_t = 1.0 +ref_t = 300 +; Pressure coupling = +Pcoupl = Parrinello-Rahman +tau_p = 4.0 +compressibility = 4.5e-5 +ref_p = 1.0 + +;lincs-iter = 2 +;lincs-order = 8 + +;-------------------- +; Free energy parameters +free-energy = yes +sc-power = 1 +sc-alpha = 0.5 +sc-sigma = 0.3 +sc-r-power = 6 + +; Which intermediate state do we start with? Doesn't really matter, it leaves soon +;------- +init-lambda-state = 0.0 + +; What are the values of lambda at the intermediate states? +;------- +fep_lambdas = 0 + +; This makes sure we print out the differences in Hamiltonians between all states, and not just the neighboring states +;-------- +calc-lambda-neighbors = -1 + +; the frequency the free energy information is calculated. This +; frequency (every 0.2 ps) is pretty good for small molecule solvation. +;------- +nstdhdl = 10 + +; not required, but useful if you are doing any temperature reweighting. Without +; temperature reweighting, you don't need the total energy -- differences are enough +dhdl-print-energy = yes + +; We are doing free energies with the solute molecule alone +couple-moltype = SOLUTE + +separate-dhdl-file = yes + +; decharging free energy +; couple-lambda0 = vdw-q +; couple-lambda1 = vdw +; LJ decoupling free energy +; couple-lambda0 = vdw +; couple-lambda1 = none +; +; fully coupled (change for BAR!) +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q + +; we are keeping the intramolecular interactions ON in all the interactions from state 0 to state 8 +couple-intramol = no diff --git a/doc/examples/martini/water.gro b/doc/examples/martini/water.gro new file mode 100644 index 00000000..81cc49ef --- /dev/null +++ b/doc/examples/martini/water.gro @@ -0,0 +1,2707 @@ +Bulk water + 2704 + 2W W 9 0.623 6.453 2.746 -0.0737 -0.1789 -0.1413 + 3W W 10 1.495 0.821 3.127 -0.1418 -0.1647 0.0677 + 4W W 11 2.276 4.379 0.851 0.2728 0.0220 0.2236 + 5W W 12 5.055 4.688 2.860 0.0937 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b/doc/sphinx/source/conf.py index b55c6df5..df741327 100644 --- a/doc/sphinx/source/conf.py +++ b/doc/sphinx/source/conf.py @@ -55,9 +55,8 @@ # General information about the project. project = "MDPOW" now = datetime.datetime.now() -copyright = "2010–{}, Shujie Fan, Ian Kenney, Alia Lescoulie, Bogdan Iorga, and Oliver Beckstein".format( - now.year -) +authors = "Shujie Fan, Ian Kenney, Alia Lescoulie, Bogdan Iorga, and Oliver Beckstein" +copyright = "2010–{}, ".format(now.year) + authors # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -220,16 +219,16 @@ latex_documents = [ ( "index", - "MDpow.tex", - "MDpow Documentation", - "Ian Kenney, Bogdan Iorga, and Oliver Beckstein", + "MDPOW.tex", + "MDPOW Documentation", + authors, "manual", ), ] # The name of an image file (relative to this directory) to place at the top of # the title page. -# latex_logo = None +latex_logo = html_logo # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. @@ -250,17 +249,16 @@ # intersphinx: reference standard lib and RecSQL # http://sphinx.pocoo.org/latest/ext/intersphinx.html intersphinx_mapping = { - "https://docs.python.org/": None, - "https://numpy.org/doc/stable/": None, - "https://docs.scipy.org/doc/scipy/reference/": None, - "https://gromacswrapper.readthedocs.io/en/latest": None, - "https://docs.mdanalysis.org/stable/": None, - "https://www.rdkit.org/docs/": None, - "https://pandas.pydata.org/docs/": None, - "https://seaborn.pydata.org": None, - "https://cairosvg.org/documentation/": None, - "https://svgutils.readthedocs.io/en/latest/": None, - "https://pypdf.readthedocs.io/en/stable/": None, + "python": ("https://docs.python.org/3", None), + "numpy": ("https://numpy.org/doc/stable/", None), + "scipy": ("https://docs.scipy.org/doc/scipy", None), + "GromacsWrapper": ("https://gromacswrapper.readthedocs.io/en/latest", None), + "MDAnalysis": ("https://docs.mdanalysis.org/stable/", None), + "RDKit": ("https://www.rdkit.org/docs/", None), + "pandas": ("https://pandas.pydata.org/docs/", None), + "seaborn": ("https://seaborn.pydata.org", None), + "svgutils": ("https://svgutils.readthedocs.io/en/latest/", None), + "pypdf": ("https://pypdf.readthedocs.io/en/stable/", None), } diff --git a/doc/sphinx/source/index.txt b/doc/sphinx/source/index.txt index b5a3d884..a1802482 100644 --- a/doc/sphinx/source/index.txt +++ b/doc/sphinx/source/index.txt @@ -46,7 +46,8 @@ software package [#GromacsWrapperFramework]_. MDPOW is tested with * Gromacs 2020.6 * Gromacs 2021.1 * Gromacs 2022.4 -* Gromacs 2023.1 +* Gromacs 2023.1 +* Gromacs 2024.3 but versions 5.x, 2016.x, and 2019.x should also work. It should be possible to use any of these Gromacs versions without diff --git a/doc/sphinx/source/init.txt b/doc/sphinx/source/init.txt index f07aa47f..23e071fb 100644 --- a/doc/sphinx/source/init.txt +++ b/doc/sphinx/source/init.txt @@ -312,7 +312,7 @@ Hydration free energy Reopen the python session and set up a :class:`~mdpow.fep.Ghyd` object:: import mdpow.fep - gwat = mdpow.fep.Ghyd(molecule="OcOH", top="Equilibrium/water/top/system.top", struct="Equilibrium/water/MD_NPT/md.pdb", ndx="Equilibrium/water/solvation/main.ndx", runtime=100) + gwat = mdpow.fep.Ghyd(molecule="OcOH", top="Equilibrium/water/top/system.top.template", struct="Equilibrium/water/MD_NPT/md.pdb", ndx="Equilibrium/water/solvation/main.ndx", runtime=100) Alternatively, one can save some typing if we continue the last session and use the :class:`mdpow.equil.Simulation` object (which we can re-load from its saved diff --git a/mdpow/__init__.py b/mdpow/__init__.py index 371ec35f..87c9f11f 100644 --- a/mdpow/__init__.py +++ b/mdpow/__init__.py @@ -52,3 +52,7 @@ def log_banner(logger): N_AVOGADRO = 6.02214179e23 #: Boltzmann's constant |kB| in kJ mol^-1 (`kB NIST value`_). kBOLTZ = 1.3806504e-23 * 1e-3 * N_AVOGADRO + +from . import _version + +__version__ = _version.get_versions()["version"] diff --git a/mdpow/_version.py b/mdpow/_version.py index e5328388..b2d97113 100644 --- a/mdpow/_version.py +++ b/mdpow/_version.py @@ -4,18 +4,22 @@ # directories (produced by setup.py build) will contain a much shorter file # that just contains the computed version number. -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) +# This file is released into the public domain. +# Generated by versioneer-0.29 +# https://github.com/python-versioneer/python-versioneer """Git implementation of _version.py.""" + import errno import os import re import subprocess import sys +from typing import Any, Callable, Dict, List, Optional, Tuple +import functools -def get_keywords(): +def get_keywords() -> Dict[str, str]: """Get the keywords needed to look up the version information.""" # these strings will be replaced by git during git-archive. # setup.py/versioneer.py will grep for the variable names, so they must @@ -31,8 +35,15 @@ def get_keywords(): class VersioneerConfig: """Container for Versioneer configuration parameters.""" + VCS: str + style: str + tag_prefix: str + parentdir_prefix: str + versionfile_source: str + verbose: bool + -def get_config(): +def get_config() -> VersioneerConfig: """Create, populate and return the VersioneerConfig() object.""" # these strings are filled in when 'setup.py versioneer' creates # _version.py @@ -50,14 +61,14 @@ class NotThisMethod(Exception): """Exception raised if a method is not valid for the current scenario.""" -LONG_VERSION_PY = {} -HANDLERS = {} +LONG_VERSION_PY: Dict[str, str] = {} +HANDLERS: Dict[str, Dict[str, Callable]] = {} -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" +def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator + """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): + def decorate(f: Callable) -> Callable: """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} @@ -67,24 +78,39 @@ def decorate(f): return decorate -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): +def run_command( + commands: List[str], + args: List[str], + cwd: Optional[str] = None, + verbose: bool = False, + hide_stderr: bool = False, + env: Optional[Dict[str, str]] = None, +) -> Tuple[Optional[str], Optional[int]]: """Call the given command(s).""" assert isinstance(commands, list) - p = None - for c in commands: + process = None + + popen_kwargs: Dict[str, Any] = {} + if sys.platform == "win32": + # This hides the console window if pythonw.exe is used + startupinfo = subprocess.STARTUPINFO() + startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW + popen_kwargs["startupinfo"] = startupinfo + + for command in commands: try: - dispcmd = str([c] + args) + dispcmd = str([command] + args) # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen( - [c] + args, + process = subprocess.Popen( + [command] + args, cwd=cwd, env=env, stdout=subprocess.PIPE, stderr=(subprocess.PIPE if hide_stderr else None), + **popen_kwargs, ) break - except EnvironmentError: - e = sys.exc_info()[1] + except OSError as e: if e.errno == errno.ENOENT: continue if verbose: @@ -95,18 +121,20 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= if verbose: print("unable to find command, tried %s" % (commands,)) return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: + stdout = process.communicate()[0].strip().decode() + if process.returncode != 0: if verbose: print("unable to run %s (error)" % dispcmd) print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode + return None, process.returncode + return stdout, process.returncode -def versions_from_parentdir(parentdir_prefix, root, verbose): +def versions_from_parentdir( + parentdir_prefix: str, + root: str, + verbose: bool, +) -> Dict[str, Any]: """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both @@ -115,7 +143,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): """ rootdirs = [] - for i in range(3): + for _ in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): return { @@ -125,9 +153,8 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): "error": None, "date": None, } - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level + rootdirs.append(root) + root = os.path.dirname(root) # up a level if verbose: print( @@ -138,41 +165,48 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): @register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): +def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. - keywords = {} + keywords: Dict[str, str] = {} try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: + with open(versionfile_abs, "r") as fobj: + for line in fobj: + if line.strip().startswith("git_refnames ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["refnames"] = mo.group(1) + if line.strip().startswith("git_full ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["full"] = mo.group(1) + if line.strip().startswith("git_date ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["date"] = mo.group(1) + except OSError: pass return keywords @register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): +def git_versions_from_keywords( + keywords: Dict[str, str], + tag_prefix: str, + verbose: bool, +) -> Dict[str, Any]: """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") + if "refnames" not in keywords: + raise NotThisMethod("Short version file found") date = keywords.get("date") if date is not None: + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] + # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 # -like" string, which we must then edit to make compliant), because @@ -185,11 +219,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) + refs = {r.strip() for r in refnames.strip("()").split(",")} # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) + tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -198,7 +232,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r"\d", r)]) + tags = {r for r in refs if re.search(r"\d", r)} if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: @@ -207,6 +241,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): r = ref[len(tag_prefix) :] + # Filter out refs that exactly match prefix or that don't start + # with a number once the prefix is stripped (mostly a concern + # when prefix is '') + if not re.match(r"\d", r): + continue if verbose: print("picking %s" % r) return { @@ -229,7 +268,9 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): @register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): +def git_pieces_from_vcs( + tag_prefix: str, root: str, verbose: bool, runner: Callable = run_command +) -> Dict[str, Any]: """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* @@ -240,7 +281,14 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) + # GIT_DIR can interfere with correct operation of Versioneer. + # It may be intended to be passed to the Versioneer-versioned project, + # but that should not change where we get our version from. + env = os.environ.copy() + env.pop("GIT_DIR", None) + runner = functools.partial(runner, env=env) + + _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose) if rc != 0: if verbose: print("Directory %s not under git control" % root) @@ -248,7 +296,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command( + describe_out, rc = runner( GITS, [ "describe", @@ -257,7 +305,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): "--always", "--long", "--match", - "%s*" % tag_prefix, + f"{tag_prefix}[[:digit:]]*", ], cwd=root, ) @@ -265,16 +313,48 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if describe_out is None: raise NotThisMethod("'git describe' failed") describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) + full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) if full_out is None: raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() - pieces = {} + pieces: Dict[str, Any] = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None + branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root) + # --abbrev-ref was added in git-1.6.3 + if rc != 0 or branch_name is None: + raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") + branch_name = branch_name.strip() + + if branch_name == "HEAD": + # If we aren't exactly on a branch, pick a branch which represents + # the current commit. If all else fails, we are on a branchless + # commit. + branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) + # --contains was added in git-1.5.4 + if rc != 0 or branches is None: + raise NotThisMethod("'git branch --contains' returned error") + branches = branches.split("\n") + + # Remove the first line if we're running detached + if "(" in branches[0]: + branches.pop(0) + + # Strip off the leading "* " from the list of branches. + branches = [branch[2:] for branch in branches] + if "master" in branches: + branch_name = "master" + elif not branches: + branch_name = None + else: + # Pick the first branch that is returned. Good or bad. + branch_name = branches[0] + + pieces["branch"] = branch_name + # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] # TAG might have hyphens. git_describe = describe_out @@ -291,7 +371,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # TAG-NUM-gHEX mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) if not mo: - # unparseable. Maybe git-describe is misbehaving? + # unparsable. Maybe git-describe is misbehaving? pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out return pieces @@ -317,26 +397,27 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): else: # HEX: no tags pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) - pieces["distance"] = int(count_out) # total number of commits + out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) + pieces["distance"] = len(out.split()) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[ - 0 - ].strip() + date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces -def plus_or_dot(pieces): +def plus_or_dot(pieces: Dict[str, Any]) -> str: """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" -def render_pep440(pieces): +def render_pep440(pieces: Dict[str, Any]) -> str: """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you @@ -360,23 +441,70 @@ def render_pep440(pieces): return rendered -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. +def render_pep440_branch(pieces: Dict[str, Any]) -> str: + """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . + + The ".dev0" means not master branch. Note that .dev0 sorts backwards + (a feature branch will appear "older" than the master branch). Exceptions: - 1: no tags. 0.post.devDISTANCE + 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0" + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: + """Split pep440 version string at the post-release segment. + + Returns the release segments before the post-release and the + post-release version number (or -1 if no post-release segment is present). + """ + vc = str.split(ver, ".post") + return vc[0], int(vc[1] or 0) if len(vc) == 2 else None + + +def render_pep440_pre(pieces: Dict[str, Any]) -> str: + """TAG[.postN.devDISTANCE] -- No -dirty. + + Exceptions: + 1: no tags. 0.post0.devDISTANCE + """ + if pieces["closest-tag"]: if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] + # update the post release segment + tag_version, post_version = pep440_split_post(pieces["closest-tag"]) + rendered = tag_version + if post_version is not None: + rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) + else: + rendered += ".post0.dev%d" % (pieces["distance"]) + else: + # no commits, use the tag as the version + rendered = pieces["closest-tag"] else: # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] + rendered = "0.post0.dev%d" % pieces["distance"] return rendered -def render_pep440_post(pieces): +def render_pep440_post(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards @@ -403,12 +531,41 @@ def render_pep440_post(pieces): return rendered -def render_pep440_old(pieces): +def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: + """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . + + The ".dev0" means not master branch. + + Exceptions: + 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + rendered += ".post%d" % pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "g%s" % pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0.post%d" % pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+g%s" % pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def render_pep440_old(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. - Eexceptions: + Exceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: @@ -425,7 +582,7 @@ def render_pep440_old(pieces): return rendered -def render_git_describe(pieces): +def render_git_describe(pieces: Dict[str, Any]) -> str: """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. @@ -445,7 +602,7 @@ def render_git_describe(pieces): return rendered -def render_git_describe_long(pieces): +def render_git_describe_long(pieces: Dict[str, Any]) -> str: """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. @@ -465,7 +622,7 @@ def render_git_describe_long(pieces): return rendered -def render(pieces, style): +def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: """Render the given version pieces into the requested style.""" if pieces["error"]: return { @@ -481,10 +638,14 @@ def render(pieces, style): if style == "pep440": rendered = render_pep440(pieces) + elif style == "pep440-branch": + rendered = render_pep440_branch(pieces) elif style == "pep440-pre": rendered = render_pep440_pre(pieces) elif style == "pep440-post": rendered = render_pep440_post(pieces) + elif style == "pep440-post-branch": + rendered = render_pep440_post_branch(pieces) elif style == "pep440-old": rendered = render_pep440_old(pieces) elif style == "git-describe": @@ -503,7 +664,7 @@ def render(pieces, style): } -def get_versions(): +def get_versions() -> Dict[str, Any]: """Get version information or return default if unable to do so.""" # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have # __file__, we can work backwards from there to the root. Some @@ -523,7 +684,7 @@ def get_versions(): # versionfile_source is the relative path from the top of the source # tree (where the .git directory might live) to this file. Invert # this to find the root from __file__. - for i in cfg.versionfile_source.split("/"): + for _ in cfg.versionfile_source.split("/"): root = os.path.dirname(root) except NameError: return { diff --git a/mdpow/equil.py b/mdpow/equil.py index d1ac36ff..82a806e2 100644 --- a/mdpow/equil.py +++ b/mdpow/equil.py @@ -29,9 +29,13 @@ .. autodata:: DIST """ import pickle +import re import os, errno import shutil +from pathlib import Path +from string import Template +from typing import Union import MDAnalysis as mda @@ -139,7 +143,12 @@ class Simulation(Journalled): "energy_minimize": "em_opls.mdp", } - def __init__(self, molecule=None, **kwargs): + def __init__( + self, + molecule=None, + forcefield: Union[forcefields.Forcefield, str] = "OPLS-AA", + **kwargs, + ): """Set up Simulation instance. The *molecule* of the compound molecule should be supplied. Existing files @@ -156,14 +165,17 @@ def __init__(self, molecule=None, **kwargs): *dirname* base directory; all other directories are created under it *forcefield* - 'OPLS-AA' or 'CHARMM' or 'AMBER' + A :class:`~forcefields.Forcefield`, or the string name of a + packaged forcefield: 'OPLS-AA', 'CHARMM' or 'AMBER'. *solvent* 'water' or 'octanol' or 'cyclohexane' or 'wetoctanol' or 'toluene' *solventmodel* - ``None`` chooses the default (e.g, :data:`mdpow.forcefields.DEFAULT_WATER_MODEL` - for ``solvent == "water"``. Other options are the models defined in - :data:`mdpow.forcefields.GROMACS_WATER_MODELS`. At the moment, there are no - alternative parameterizations included for other solvents. + ``None`` chooses the default (e.g, the + :class:`mdpow.forcefields.Forcefield` default water model for + ``solvent == "water"``. Other options are the models defined in + :data:`mdpow.forcefields.GROMACS_WATER_MODELS`. At the moment, + there are no alternative parameterizations included for other + solvents. *mdp* dict with keys corresponding to the stages ``energy_minimize``, ``MD_restrained``, ``MD_relaxed``, @@ -175,12 +187,16 @@ def __init__(self, molecule=None, **kwargs): advanced keywords for short-circuiting; see :data:`mdpow.equil.Simulation.filekeys`. + .. versionchanged:: 0.9.0 + `forcefield` may now be either a :class:`~forcefields.Forcefield` or + the string name of a builtin forcefield. + """ self.__cache = {} filename = kwargs.pop("filename", None) dirname = kwargs.pop("dirname", self.dirname_default) - forcefield = kwargs.pop("forcefield", "OPLS-AA") + forcefield = forcefields.get_forcefield(forcefield) solvent = kwargs.pop("solvent", self.solvent_default) # mdp files --- should get values from default runinput.cfg # None values in the kwarg mdp dict are ignored @@ -350,11 +366,21 @@ def topology(self, itp="drug.itp", prm=None, **kwargs): dirname = kwargs.pop("dirname", self.BASEDIR("top")) self.dirs.topology = realpath(dirname) - setting = forcefields.get_ff_paths(self.forcefield) template = forcefields.get_top_template(self.solvent_type) top_template = config.get_template(kwargs.pop("top_template", template)) - topol = kwargs.pop("topol", os.path.basename(top_template)) + + default_top_path = Path(top_template) + if ".top" in default_top_path.suffixes: + # Include all suffixes up to that one + default_top_name = default_top_path.name + default_top_name = ( + default_top_name[: default_top_name.index(".top")] + ".top" + ) + else: + default_top_name = default_top_path.with_suffix(".top").name + + topol = kwargs.pop("topol", default_top_name) self.top_template = top_template itp = os.path.realpath(itp) _itp = os.path.basename(itp) @@ -367,40 +393,23 @@ def topology(self, itp="drug.itp", prm=None, **kwargs): prm_kw = '#include "{}"'.format(_prm) with in_dir(dirname): + with open(top_template, "r") as f: + top_string_template = Template(f.read()) + top_string_formatted = top_string_template.substitute( + forcefield_itp=self.forcefield.forcefield_dir / "forcefield.itp", + prm_line=f'#include "{prm_kw}"' if prm_kw else "", + compound_itp=_itp, + solvent_itp=self.forcefield.forcefield_dir / self.solvent.itp, + ions_itp=self.forcefield.ions_itp, + water_itp=self.forcefield.default_water_itp, + compound_name=self.molecule, + solvent=self.solvent_type, + ) + with open(topol, "w") as f: + f.write(top_string_formatted) shutil.copy(itp, _itp) if prm is not None: shutil.copy(prm, _prm) - gromacs.cbook.edit_txt( - top_template, - [ - ( - r'#include +"oplsaa\.ff/forcefield\.itp"', - r"oplsaa\.ff/", - setting[0], - ), - (r'#include +"compound\.itp"', r"compound\.itp", _itp), - ( - r'#include +"oplsaa\.ff/tip4p\.itp"', - r"oplsaa\.ff/tip4p\.itp", - setting[0] + self.solvent.itp, - ), - ( - r'#include +"oplsaa\.ff/ions_opls\.itp"', - r"oplsaa\.ff/ions_opls\.itp", - setting[1], - ), - ( - r'#include +"compound\.prm"', - r'#include +"compound\.prm"', - prm_kw, - ), - (r'#include +"water\.itp"', r"water\.itp", setting[2]), - (r"Compound", "solvent", self.solvent_type), - (r"Compound", "DRUG", self.molecule), - (r"DRUG\s*1", "DRUG", self.molecule), - ], - newname=topol, - ) logger.info( "[%(dirname)s] Created topology %(topol)r that includes %(_itp)r", vars() ) @@ -526,9 +535,8 @@ def _MD(self, protocol, **kwargs): kwargs["top"] = self.files.topology kwargs["includes"] = asiterable(kwargs.pop("includes", [])) + self.dirs.includes kwargs["ndx"] = self.files.ndx - kwargs[ - "mainselection" - ] = None # important for SD (use custom mdp and ndx!, gromacs.setup._MD) + # important for SD (use custom mdp and ndx!, gromacs.setup._MD): + kwargs["mainselection"] = None self._checknotempty(kwargs["struct"], "struct") if not os.path.exists(kwargs["struct"]): # struct is not reliable as it depends on qscript so now we just try everything... diff --git a/mdpow/fep.py b/mdpow/fep.py index 4edd0362..b3b14d00 100644 --- a/mdpow/fep.py +++ b/mdpow/fep.py @@ -1020,7 +1020,7 @@ def analyze(self, force=False, stride=None, autosave=True, ncorrel=25000): The dV/dlambda graphs are integrated with the composite Simpson's rule (and if the number of datapoints are even, the first interval is - evaluated with the trapezoidal rule); see :func:`scipy.integrate.simps` + evaluated with the trapezoidal rule); see :func:`scipy.integrate.simpson` for details). Note that this implementation of Simpson's rule does not require equidistant spacing on the lambda axis. @@ -1081,6 +1081,14 @@ def analyze(self, force=False, stride=None, autosave=True, ncorrel=25000): Diego 2002 .. _p526: http://books.google.co.uk/books?id=XmyO2oRUg0cC&pg=PA526 + + .. versionchanged:: 0.9.0 + Change in how the Simpson's rule integration algorithm (namely, + :func:`scipy.integrate.simpson`) handles even number of intervals: + Previously, the old `even="last"` was used but since scipy 1.11.0 + Cartwright's approach is used. This change **leads to numerically + slightly different results** between MDPOW 0.9.0 and earlier + versions. """ stride = stride or self.stride logger.info("Analysis stride is %s.", stride) @@ -1137,9 +1145,11 @@ def analyze(self, force=False, stride=None, autosave=True, ncorrel=25000): "tcorrel": tc, } # Combined Simpson rule integration: - # even="last" because dV/dl is smoother at the beginning so using trapezoidal - # integration there makes less of an error (one hopes...) - a = scipy.integrate.simps(Y, x=lambdas, even="last") + # Used to have 'even="last"' because dV/dl is smoother at the beginning so + # using trapezoidal integration there makes less of an error (one hopes...) + # but recent versions of scipy (eg 1.14) always use Cartwright's approach + # for the last interval and "even" is not a kwarg anymore. + a = scipy.integrate.simpson(Y, x=lambdas) da = numkit.integration.simps_error(DY, x=lambdas, even="last") self.results.DeltaA[component] = QuantityWithError(a, da) GibbsFreeEnergy += self.results.DeltaA[ @@ -1179,7 +1189,6 @@ def collect_alchemlyb( for l in lambdas: xvg_file = self.dgdl_xvg(self.wdir(component, l)) xvg_df = extract(xvg_file, T=self.Temperature).iloc[start:stop:stride] - full_len = len(xvg_df) if SI: logger.info( "Performing statistical inefficiency analysis for window %s %04d" @@ -1190,16 +1199,6 @@ def collect_alchemlyb( ts = ts.set_index("time") # use the statistical_inefficiency function to subsample the data xvg_df = statistical_inefficiency(xvg_df, ts, conservative=True) - logger.info( - "The statistical inefficiency value is {:.4f}.".format( - full_len / len(xvg_df) / 2 - ) - ) - logger.info( - "The data are subsampled every {:d} frames.".format( - int(np.ceil(full_len / len(xvg_df) / 2)) - ) - ) val.append(xvg_df) self.results.xvg[component] = (np.array(lambdas), pd.concat(val)) diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 348944da..7b15c04d 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -12,12 +12,12 @@ different force fields and the corresponding solvent topologies. The OPLS-AA, CHARMM/CGENFF and the AMBER/GAFF force field are directly -supported. In the principle it is possible to switch to a -different force field by supplying alternative template -files. +supported. It is possible to use a different forcefield by implementing +a :class:`Forcefield` with the correct files and supplying suitable +``.mdp`` files. For an example of how to do this, look at the +``martini-example.ipynb`` under ``doc/examples/martini-example``. .. autodata:: DEFAULT_FORCEFIELD -.. autodata:: DEFAULT_WATER_MODEL Solvent models @@ -40,6 +40,8 @@ :noindex: .. autodata:: GROMACS_SOLVENT_MODELS :noindex: +.. autodata:: ALL_FORCEFIELDS + :noindex: Internal classes and functions ------------------------------ @@ -47,6 +49,9 @@ .. autoclass:: GromacsSolventModel :members: +.. autoclass:: Forcefield + :members: + .. autofunction:: get_water_model .. autofunction:: get_solvent_identifier @@ -55,55 +60,44 @@ """ import os +from dataclasses import dataclass from collections import defaultdict +from pathlib import Path +from typing import Dict, List, Union, Optional import logging +from . import config + logger = logging.getLogger("mdpow.forecefields") +Pathy = Union[str, os.PathLike] #: Default force field. At the moment, OPLS-AA, CHARMM/CGENFF, and AMBER/GAFF #: are directly supported. However, it is not recommended to change the #: default here as this behavior is not tested. DEFAULT_FORCEFIELD = "OPLS-AA" -# ------------------------------------------------------------ -# Gromacs water models -# ------------------------------------------------------------ -#: See the file ``top/oplsaa.ff/watermodels.dat`` for a description of -#: available water models that are bundled with MDPOW. -GMX_WATERMODELS_DAT = """ -tip4p TIP4P TIP 4-point, recommended -tip3p TIP3P TIP 3-point -tip5p TIP5P TIP 5-point -spc SPC simple point charge -spce SPC/E extended simple point charge -m24 M24 TIP 3-point with modified LJ (M24) -tip4pd TIP4P-D TIP 4-point with modified dispersion (TIP4P-D) -tip4pew TIP4PEW TIP 4-point modified for use with Ewald techniques (TIP4PEW) -""" - - -class GromacsSolventModel(object): +@dataclass +class GromacsSolventModel: """Data for a solvent model in Gromacs.""" - def __init__( + identifier: str + name: Optional[str] = None + itp: Optional[Pathy] = None + coordinates: Optional[Pathy] = None + description: Optional[str] = None + forcefield: str = "OPLS-AA" + + def __post_init__( self, - identifier, - name=None, - itp=None, - coordinates=None, - description=None, - forcefield="OPLS-AA", ): - self.identifier = identifier - self.name = name if name is not None else str(identifier).upper() - self.itp = itp if itp is not None else self.guess_filename("itp") - self.coordinates = ( - coordinates if coordinates is not None else self.guess_filename("gro") - ) - self.description = description - self.forcefield = forcefield + if self.name is None: + self.name = str(self.identifier).upper() + if self.itp is None: + self.itp = self.guess_filename("itp") + if self.coordinates is None: + self.coordinates = self.guess_filename("gro") def guess_filename(self, extension): """Guess the filename for the model and add *extension*""" @@ -117,6 +111,22 @@ def __repr__(self): ) +# ------------------------------------------------------------ +# Gromacs water models +# ------------------------------------------------------------ + +#: See the file ``top/oplsaa.ff/watermodels.dat`` for a description of +#: available water models that are bundled with MDPOW. +GMX_WATERMODELS_DAT = """ +tip4p TIP4P TIP 4-point, recommended +tip3p TIP3P TIP 3-point +tip5p TIP5P TIP 5-point +spc SPC simple point charge +spce SPC/E extended simple point charge +m24 M24 TIP 3-point with modified LJ (M24) +tip4pd TIP4P-D TIP 4-point with modified dispersion (TIP4P-D) +tip4pew TIP4PEW TIP 4-point modified for use with Ewald techniques (TIP4PEW) +""" #: For some water models we cannot derive the filename for the equilibrated box #: so we supply them explicitly. SPECIAL_WATER_COORDINATE_FILES = defaultdict( @@ -130,9 +140,10 @@ def __repr__(self): ) -def _create_water_models(watermodelsdat): +def _create_water_models(watermodelsdat: Path) -> Dict[str, GromacsSolventModel]: models = {} - for line in GMX_WATERMODELS_DAT.split("\n"): + data = watermodelsdat.read_text() + for line in data.split("\n"): line = line.strip() if not line or line.startswith("#"): continue @@ -148,26 +159,66 @@ def _create_water_models(watermodelsdat): return models -#: Use the default water model unless another water model is chosen in the -#: :ref:`run input file ` file by setting the -#: ``setup.watermodel`` parameter. -#: -#: .. warning:: -#: Select the native water model **manually** and do not rely on the default -#: set here. For CHARMM/GAFF the CHARMM TIP3P model is recommended. -#: For AMBER/GAFF the TIP3P mdeol is often used. Choosing the correct water model -#: is a *scientific* decision that *you* have to make conscientiously. -#: -DEFAULT_WATER_MODEL = "tip4p" +#: See the file ``top/oplsaa.ff/watermodels.dat`` for a description of +#: available water models that are bundled with MDPOW. #: Dictionary of :class:`GromacsSolventModel` instances, one for each Gromacs water #: model available under the force field directory. The keys are the water model #: identifiers. #: For OPLS-AA the following ones are available. -GROMACS_WATER_MODELS = _create_water_models(GMX_WATERMODELS_DAT) +GROMACS_WATER_MODELS: Dict[str, GromacsSolventModel] = { + "tip4p": GromacsSolventModel( + "tip4p", + name="TIP4P", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip4p"], + description="TIP 4-point, recommended", + ), + "tip3p": GromacsSolventModel( + "tip3p", + name="TIP3P", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip3p"], + description="TIP 3-point", + ), + "tip5p": GromacsSolventModel( + "tip5p", + name="TIP5P", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip5p"], + description="TIP 5-point", + ), + "spc": GromacsSolventModel( + "spc", + name="SPC", + coordinates=SPECIAL_WATER_COORDINATE_FILES["spc"], + description="simple point charge", + ), + "spce": GromacsSolventModel( + "spce", + name="SPC/E", + coordinates=SPECIAL_WATER_COORDINATE_FILES["spce"], + description="extended simple point charge", + ), + "m24": GromacsSolventModel( + "m24", + name="M24", + coordinates=SPECIAL_WATER_COORDINATE_FILES["m24"], + description="TIP 3-point with modified LJ (M24)", + ), + "tip4pd": GromacsSolventModel( + "tip4pd", + name="TIP4P-D", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip4pd"], + description="TIP 4-point with modified dispersion (TIP4P-D)", + ), + "tip4pew": GromacsSolventModel( + "tip4pew", + name="TIP4PEW", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip4pew"], + description="TIP 4-point modified for use with Ewald techniques (TIP4PEW)", + ), +} -def get_water_model(watermodel=DEFAULT_WATER_MODEL): +def get_water_model(watermodel="tip4p"): """Return a :class:`GromacsSolventModel` corresponding to identifier *watermodel*""" try: @@ -180,78 +231,160 @@ def get_water_model(watermodel=DEFAULT_WATER_MODEL): raise ValueError(msg) +@dataclass +class Forcefield: + """Contains information about files corresponding to a forcefield. + + .. versionadded:: 0.9.0 + + """ + + name: str + solvent_models: Dict[str, GromacsSolventModel] + forcefield_dir: Path + ions_itp: Path + default_water_itp: Path + default_water_model: str = "tip4p" + water_models: Optional[Dict[str, GromacsSolventModel]] = None + + def __post_init__(self): + """Check that the provided paths exist and populate the :attr:`water_models`.""" + for path_ in self.ff_paths: + if not path_.exists(): + raise ValueError(f"Could not find required forcefield files: {path_}") + + if self.water_models is None: + self.water_models = _create_water_models( + self.forcefield_dir / "watermodels.dat" + ) + + @property + def ff_paths(self) -> List[Path]: + """Get the path to the forcefield directory and the ITP files for the ions and default water model.""" + return [self.forcefield_dir, self.ions_itp, self.default_water_itp] + + def __repr__(self) -> str: + """Get the name of the force field.""" + return self.name + + #: Other solvents (not water, see :data:`GROMACS_WATER_MODELS` for those). -new_octanol = """Zangi R (2018) Refinement of the OPLSAA force-field - for liquid alcohols.; ACS Omega 3(12):18089-18099. - doi: 10.1021/acsomega.8b03132""" +NEW_OCTANOL_DESC = "Zangi R (2018) Refinement of the OPLSAA force-field for liquid alcohols.; ACS Omega 3(12):18089-18099. doi: 10.1021/acsomega.8b03132" + +OPLS_AA_FF_DIR = Path(config.topfiles["oplsaa.ff"]) +OPLS_AA = Forcefield( + "OPLS-AA", + { + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct.gro" + ), + "octanolnew": GromacsSolventModel( + identifier="octanol", + itp="1octnew.itp", + coordinates="1oct.gro", + description=NEW_OCTANOL_DESC, + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet.gro" + ), + "wetoctanolnew": GromacsSolventModel( + identifier="wetoctanol", + itp="1octwetnew.itp", + coordinates="1octwet.gro", + description=NEW_OCTANOL_DESC, + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_oplsaa.gro" + ), + }, + OPLS_AA_FF_DIR, + OPLS_AA_FF_DIR / "ions_opls.itp", + OPLS_AA_FF_DIR / "tip4p.itp", +) -OPLS_SOLVENT_MODELS = { - "octanol": GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct.gro" - ), - "octanolnew": GromacsSolventModel( - identifier="octanol", - itp="1octnew.itp", - coordinates="1oct.gro", - description=new_octanol, - ), - "cyclohexane": GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo.gro" - ), - "wetoctanol": GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet.gro" - ), - "wetoctanolnew": GromacsSolventModel( - identifier="wetoctanol", - itp="1octwetnew.itp", - coordinates="1octwet.gro", - description=new_octanol, - ), - "toluene": GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_oplsaa.gro" - ), -} +CHARMM_FF_DIR = Path(config.topfiles["charmm36-mar2019.ff"]) +CHARMM = Forcefield( + "CHARMM", + { + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct_charmm.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_charmm.gro" + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_charmm.gro" + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_charmm.gro" + ), + }, + CHARMM_FF_DIR, + CHARMM_FF_DIR / "ions.itp", + CHARMM_FF_DIR / "tip3p.itp", + default_water_model="tip3p", +) -CHARMM_SOLVENT_MODELS = { - "octanol": GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct_charmm.gro" - ), - "wetoctanol": GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_charmm.gro" - ), - "cyclohexane": GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_charmm.gro" - ), - "toluene": GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_charmm.gro" - ), -} +AMBER_FF_DIR = Path(config.topfiles["amber99sb.ff"]) +AMBER = Forcefield( + "AMBER", + { + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct_amber.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_amber.gro" + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_amber.gro" + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_amber.gro" + ), + }, + AMBER_FF_DIR, + AMBER_FF_DIR / "ions.itp", + AMBER_FF_DIR / "tip3p.itp", + default_water_model="tip3p", +) -AMBER_SOLVENT_MODELS = { - "octanol": GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct_amber.gro" - ), - "wetoctanol": GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_amber.gro" - ), - "cyclohexane": GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_amber.gro" - ), - "toluene": GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_amber.gro" - ), +#: The builtin forcefields' names and the corresponding :class:`Forcefield` +#: instance +ALL_FORCEFIELDS: Dict[str, Forcefield] = { + "OPLS-AA": OPLS_AA, + "CHARMM": CHARMM, + "AMBER": AMBER, } #: Solvents available in GROMACS; the keys of the dictionary #: are the forcefields. GROMACS_SOLVENT_MODELS = { - "OPLS-AA": OPLS_SOLVENT_MODELS, - "CHARMM": CHARMM_SOLVENT_MODELS, - "AMBER": AMBER_SOLVENT_MODELS, + "OPLS-AA": OPLS_AA.solvent_models, + "CHARMM": CHARMM.solvent_models, + "AMBER": AMBER.solvent_models, } -def get_solvent_identifier(solvent_type, model=None, forcefield="OPLS-AA"): +def get_forcefield(ff: Union[str, Forcefield]) -> Forcefield: + """Get the :class:`Forcefield` instance corresponding to a given name. + + .. versionadded:: 0.9.0 + + """ + if isinstance(ff, Forcefield): + return ff + try: + return ALL_FORCEFIELDS[ff] + except KeyError: + raise ValueError(f"Forcefield `{ff}` not found.") + + +def get_solvent_identifier( + solvent_type, model=None, forcefield: Union[Forcefield, str] = OPLS_AA +): """Get the identifier for a solvent model. The identifier is needed to access a water model (i.e., a @@ -265,78 +398,81 @@ def get_solvent_identifier(solvent_type, model=None, forcefield="OPLS-AA"): model = get_solvent_model(identifier) - For ``solvent_type`` *water*: either provide ``None`` or "water" - for the specific ``model`` (and the default - :data:`DEFAULT_WATER_MODEL` will be selected, or a specific water - model such as "tip3p" or "spce" (see - :data:`GROMACS_WATER_MODELS`). For other "octanol" or "wetoctanol" - of OPLS-AA forcefield, the ``model`` is used to select a specific - model. For other solvents and forcefields, "model" is not required. + For ``solvent_type`` *water*: either provide ``None`` or "water" for the + specific ``model`` (and the default water model for the :class:`Forcefield` + will be selected, or a specific water model such as "tip3p" or "spce" (see + :data:`GROMACS_WATER_MODELS`). For other "octanol" or "wetoctanol" of + OPLS-AA forcefield, the ``model`` is used to select a specific model. For + other solvents and forcefields, "model" is not required. + + :Raises ValueError: If there is no identifier found for the combination. + + :Returns: An identifier + + .. versionchanged:: 0.9.0 + Raises :exc:`ValueError` instead of returning ``None``. - :Returns: Either an identifier or ``None`` """ + forcefield = get_forcefield(forcefield) if solvent_type == "water": - identifier = model if not model in (None, "water") else DEFAULT_WATER_MODEL - return identifier if identifier in GROMACS_WATER_MODELS else None - if model not in GROMACS_SOLVENT_MODELS[forcefield]: - if solvent_type in GROMACS_SOLVENT_MODELS[forcefield]: + identifier = ( + forcefield.default_water_model if model in [None, "water"] else model + ) + + if identifier in forcefield.water_models: + return identifier + else: + raise ValueError( + f"{identifier} is not a valid water model for {forcefield.name}." + ) + + if model not in forcefield.solvent_models: + if solvent_type in forcefield.solvent_models: model = solvent_type else: - model = None + raise ValueError( + f"Solvent type {solvent_type} not available in {forcefield.name} solvent models." + ) + return model -def get_solvent_model(identifier, forcefield="OPLS-AA"): +def get_solvent_model(identifier, forcefield: Union[Forcefield, str] = OPLS_AA): """Return a :class:`GromacsSolventModel` corresponding to identifier *identifier*. - If identifier is "water" then the :data:`DEFAULT_WATER_MODEL` is assumed. + If identifier is "water" then the default water model for the :class:`Forcefield` is assumed. + + .. versionchanged:: 0.9.0 + Function can now also accept a :class:`Forcefield` for the ``forcefield`` argument. + """ + forcefield = get_forcefield(forcefield) if identifier == "water": - identifier = DEFAULT_WATER_MODEL + identifier = forcefield.default_water_model try: - return GROMACS_WATER_MODELS[identifier] + return forcefield.water_models[identifier] except KeyError: try: - return GROMACS_SOLVENT_MODELS[forcefield][identifier] + return forcefield.solvent_models[identifier] except KeyError: - msg = "No solvent model with name {0} is available.".format(identifier) + msg = "No solvent model with name {0} is available for forcefield {1}.".format( + identifier, forcefield.name + ) logger.critical(msg) raise ValueError(msg) -def get_ff_paths(forcefield="OPLS-AA"): - """Return a :list: containing the forcefield directory, paths of ions - and default watermodel itp files. - """ - - settings = { - "OPLS-AA": ["oplsaa.ff/", "oplsaa.ff/ions_opls.itp", "oplsaa.ff/tip4p.itp"], - "AMBER": ["amber99sb.ff/", "amber99sb.ff/ions.itp", "amber99sb.ff/tip3p.itp"], - "CHARMM": [ - "charmm36-mar2019.ff/", - "charmm36-mar2019.ff/ions.itp", - "charmm36-mar2019.ff/tip3p.itp", - ], - } - try: - return settings[forcefield] - except KeyError: - msg = "No forcefield with name {0} is available".format(forcefield) - logger.critical(msg) - raise ValueError(msg) - - def get_top_template(identifier): """Return the topology file template suitable for the solvent model.""" templates = { - "water": "system.top", - "octanol": "system.top", - "cyclohexane": "system.top", - "wetoctanol": "system_octwet.top", - "toluene": "system.top", + "water": "system.top.template", + "octanol": "system.top.template", + "cyclohexane": "system.top.template", + "wetoctanol": "system_octwet.top.template", + "toluene": "system.top.template", } try: return templates[identifier] diff --git a/mdpow/restart.py b/mdpow/restart.py index 2b2e362a..25c09133 100644 --- a/mdpow/restart.py +++ b/mdpow/restart.py @@ -116,7 +116,7 @@ def incomplete(self): def incomplete(self, stage): if not stage in self.stages: raise ValueError( - "can only assign a registered stage from %(stages)r" % vars(self) + "Can only assign a registered stage from %(stages)r" % vars(self) ) self.__incomplete = stage @@ -143,7 +143,7 @@ def completed(self, stage): def start(self, stage): """Record that *stage* is starting.""" - if self.current is not None: + if self.current is not None and self.current != stage: errmsg = ( "Cannot start stage %s because previously started stage %s " "has not been completed." % (stage, self.current) @@ -157,7 +157,16 @@ def has_completed(self, stage): return stage in self.history def has_not_completed(self, stage): - """Returns ``True`` if the *stage* had been started but not completed yet.""" + """Returns ``True`` if the *stage* had been started but not completed yet. + + This is subtly different from ``not`` :func:`has_completed` in + that two things have to be true: + + 1. No stage is active (which is the case when a restart is attempted). + 2. The `stage` has not been completed previously (i.e., + :func:`has_completed` returns ``False``) + + """ return self.current is None and not self.has_completed(stage) def clear(self): @@ -190,13 +199,14 @@ def __init__(self, *args, **kwargs): len(self.journal.history) except AttributeError: self.journal = Journal(self.protocols) - super(Journalled, self).__init__(*args, **kwargs) + super().__init__(*args, **kwargs) def get_protocol(self, protocol): """Return method for *protocol*. - If *protocol* is a real method of the class then the method is - returned. + returned. This method should implement its own use of + :meth:`Journal.start` and :meth:`Journal.completed`. - If *protocol* is a registered protocol name but no method of the name exists (i.e. *protocol* is a "dummy protocol") then @@ -205,9 +215,12 @@ def get_protocol(self, protocol): .. function:: dummy_protocol(func, *args, **kwargs) - Runs *func* with the arguments and keywords between calls - to :meth:`Journal.start` and :meth:`Journal.completed`, - with the stage set to *protocol*. + Runs *func* with the arguments and keywords between calls to + :meth:`Journal.start` and :meth:`Journal.completed`, with the + stage set to *protocol*. + + The function should return ``True`` on success and ``False`` on + failure. - Raises a :exc:`ValueError` if the *protocol* is not registered (i.e. not found in :attr:`Journalled.protocols`). diff --git a/mdpow/templates/system.top b/mdpow/templates/system.top.template similarity index 71% rename from mdpow/templates/system.top rename to mdpow/templates/system.top.template index 21fa8baa..fefad275 100644 --- a/mdpow/templates/system.top +++ b/mdpow/templates/system.top.template @@ -6,22 +6,22 @@ ; to change it as needed. See the source mdpow/equil.py for details. ; Include forcefield parameters -#include "oplsaa.ff/forcefield.itp" +#include "$forcefield_itp" ; Include compound topology -#include "compound.prm" -#include "compound.itp" +$prm_line +#include "$compound_itp" ; Include solvent topology -#include "oplsaa.ff/tip4p.itp" +#include "$solvent_itp" ; Include topology for OPLS/AA ions -#include "oplsaa.ff/ions_opls.itp" +#include "$ions_itp" [ system ] ; Name -Compound DRUG in solvent +Compound $compound_name in $solvent [ molecules ] ; Compound #mols -DRUG 1 +$compound_name 1 diff --git a/mdpow/templates/system_octwet.top b/mdpow/templates/system_octwet.top.template similarity index 70% rename from mdpow/templates/system_octwet.top rename to mdpow/templates/system_octwet.top.template index 4c8c6054..be32d0db 100644 --- a/mdpow/templates/system_octwet.top +++ b/mdpow/templates/system_octwet.top.template @@ -6,24 +6,24 @@ ; to change it as needed. See the source mdpow/equil.py for details. ; Include forcefield parameters -#include "oplsaa.ff/forcefield.itp" +#include "$forcefield_itp" ; Include compound topology -#include "compound.prm" -#include "compound.itp" +$prm_line +#include "$compound_itp" ; Include solvent topology -#include "oplsaa.ff/tip4p.itp" -#include "water.itp" +#include "$solvent_itp" ; Include topology for OPLS/AA ions -#include "oplsaa.ff/ions_opls.itp" +#include "$ions_itp" +#include "$water_itp" [ system ] ; Name -Compound DRUG in solvent +Compound $compound_name in $solvent [ molecules ] ; Compound #mols -DRUG 1 +$compound_name 1 ;OcOH 1 diff --git a/mdpow/tests/test_analysis.py b/mdpow/tests/test_analysis.py index d4b21e22..af8421d6 100644 --- a/mdpow/tests/test_analysis.py +++ b/mdpow/tests/test_analysis.py @@ -84,9 +84,13 @@ def assert_DeltaA(G): # original values are only reproduced to 5 decimals, see PR #166" # - June 2023: in CI, >= 3.8 results differ from reference values (although # locally no changes are obvious) after ~4 decimals for unknown reasons. + # - Oct 2024: change to scipy.integrate.simpson(): use Cartwright's approach + # instead of even="last": changes the mean (DeltaA: from -3.722 to now -3.643) DeltaA = G.results.DeltaA assert_array_almost_equal( - DeltaA.Gibbs.astuple(), (-3.7217472974883794, 2.3144288928034911), decimal=3 + DeltaA.Gibbs.astuple(), + (-3.6429995060434432, 2.3141470255028795), + decimal=3, ) assert_array_almost_equal( DeltaA.coulomb.astuple(), @@ -94,7 +98,9 @@ def assert_DeltaA(G): decimal=3, ) assert_array_almost_equal( - DeltaA.vdw.astuple(), (-4.6128782195215781, 2.1942144688960972), decimal=3 + DeltaA.vdw.astuple(), + (-4.691626010966514, 2.1940230979105584), + decimal=3, ) def test_convert_edr(self, fep_benzene_directory): diff --git a/mdpow/tests/test_forcefields.py b/mdpow/tests/test_forcefields.py index bc5c3112..ee728cf4 100644 --- a/mdpow/tests/test_forcefields.py +++ b/mdpow/tests/test_forcefields.py @@ -9,6 +9,8 @@ WATERMODELS = ("tip4p", "tip3p", "tip5p", "spc", "spce", "m24", "tip4pd") SOLVENTMODELS = ("water", "cyclohexane", "octanol", "toluene") +forcefields = mdpow.forcefields + class TestIncludedForcefiels(object): @staticmethod @@ -29,6 +31,31 @@ def test_oplsaa_ff(): os.path.join("mdpow", "top", "oplsaa.ff") ) + @pytest.mark.parametrize( + "ff_str,ff_instance", + list( + forcefields.ALL_FORCEFIELDS.items() + ) # List of (ff_name, ff_instance) for all builtins + + [ + ("Violet Parr", None), # Nonexistent builtin + ], + ) + def test_get_forcefield(self, ff_str, ff_instance): + """Check that we can correctly cast a `Forcefield`.""" + if ff_instance is not None: + assert forcefields.get_forcefield(ff_str) == ff_instance + assert forcefields.get_forcefield(ff_instance) == ff_instance + else: + with pytest.raises(ValueError): + forcefields.get_forcefield(ff_str) + + @pytest.mark.parametrize( + "ff_str,ff_instance", list(forcefields.ALL_FORCEFIELDS.items()) + ) + def test_ff_repr(self, ff_str: str, ff_instance: forcefields.Forcefield): + """Test that forcefields are correctly represented by their names.""" + assert repr(ff_instance) == ff_str + class TestIncludedSolvents(object): solvents = { @@ -63,7 +90,7 @@ def test_solvent(self, solvent_name): class TestWatermodels(object): @staticmethod def test_default_water_model(): - assert mdpow.forcefields.DEFAULT_WATER_MODEL == "tip4p" + assert mdpow.forcefields.OPLS_AA.default_water_model == "tip4p" def test_watermodelsdat(self): included_watermodels = open(mdpow.config.topfiles["watermodels.dat"]).read() @@ -93,7 +120,7 @@ def _simple_line_parser(string): @staticmethod def test_get_water_model(): - model = mdpow.forcefields.DEFAULT_WATER_MODEL + model = mdpow.forcefields.OPLS_AA.default_water_model assert ( mdpow.forcefields.get_water_model(model) is mdpow.forcefields.GROMACS_WATER_MODELS[model] @@ -109,10 +136,10 @@ class TestSolventModels(object): @staticmethod def test_get_solvent_default_water(): model = "water" - defaultmodel = mdpow.forcefields.DEFAULT_WATER_MODEL + defaultmodel = mdpow.forcefields.OPLS_AA.default_water_model assert ( mdpow.forcefields.get_solvent_model(model) - is mdpow.forcefields.GROMACS_WATER_MODELS[defaultmodel] + == mdpow.forcefields.GROMACS_WATER_MODELS[defaultmodel] ) @staticmethod @@ -157,7 +184,7 @@ def test_get_solvent_toluene(self, forcefield): def test_get_solvent_identifier_default_is_water(): assert ( mdpow.forcefields.get_solvent_identifier("water") - is mdpow.forcefields.DEFAULT_WATER_MODEL + is mdpow.forcefields.OPLS_AA.default_water_model ) @pytest.mark.parametrize("model", WATERMODELS) @@ -174,5 +201,7 @@ def test_get_solvent_identifier_solvents(self, solvent, model): @staticmethod def test_get_solvent_identifier_None(): - assert mdpow.forcefields.get_solvent_identifier("water", model="foobar") is None - assert mdpow.forcefields.get_solvent_identifier("benzene") is None + with pytest.raises(ValueError): + mdpow.forcefields.get_solvent_identifier("water", model="foobar") + with pytest.raises(ValueError): + mdpow.forcefields.get_solvent_identifier("benzene") diff --git a/mdpow/tests/test_journals.py b/mdpow/tests/test_journals.py new file mode 100644 index 00000000..f324fa7e --- /dev/null +++ b/mdpow/tests/test_journals.py @@ -0,0 +1,175 @@ +import pytest + +from mdpow import restart + + +@pytest.fixture +def journal(): + return restart.Journal(["pre", "main", "post"]) + + +class TestJournal: + def test_full_sequence(self, journal): + journal.start("pre") + assert journal.current == "pre" + journal.completed("pre") + + journal.start("main") + assert journal.current == "main" + journal.completed("main") + + journal.start("post") + assert journal.current == "post" + journal.completed("post") + + def test_set_wrong_stage_ValueError(self, journal): + with pytest.raises(ValueError, match="Can only assign a registered stage"): + journal.start("BEGIN !") + + def test_JournalSequenceError_no_completion(self, journal): + with pytest.raises(restart.JournalSequenceError, match="Cannot start stage"): + journal.start("pre") + assert journal.current == "pre" + + journal.start("main") + + @pytest.mark.xfail + def test_JournalSequenceError_skip_stage(self, journal): + # Currently allows skipping a stage and does not enforce ALL previous + # stages to have completed. + with pytest.raises(restart.JournalSequenceError, match="Cannot start stage"): + journal.start("pre") + assert journal.current == "pre" + journal.completed("pre") + + journal.start("post") + + def test_start_idempotent(self, journal): + # test that start() can be called multiple time (#278) + journal.start("pre") + journal.start("pre") + assert journal.current == "pre" + + def test_incomplete_known_stage(self, journal): + journal.incomplete = "main" + assert journal.incomplete == "main" + + def test_incomplete_unknown_stage_ValueError(self, journal): + with pytest.raises(ValueError, match="Can only assign a registered stage from"): + journal.incomplete = "BEGIN !" + + def test_clear(self, journal): + journal.start("pre") + journal.completed("pre") + journal.start("main") + # manually setting incomplete + journal.incomplete = journal.current + + assert journal.current == "main" + assert journal.incomplete == journal.current + + journal.clear() + assert journal.current is None + assert journal.incomplete is None + + def test_history(self, journal): + journal.start("pre") + journal.completed("pre") + journal.start("main") + journal.completed("main") + journal.start("post") + + # completed stages + assert journal.history == ["pre", "main"] + + def test_history_del(self, journal): + journal.start("pre") + journal.completed("pre") + journal.start("main") + journal.completed("main") + assert journal.history + + del journal.history + assert journal.history == [] + + def test_has_completed(self, journal): + journal.start("pre") + journal.completed("pre") + + assert journal.has_completed("pre") + assert not journal.has_completed("main") + + def test_has_not_completed(self, journal): + journal.start("pre") + journal.completed("pre") + journal.start("main") + # simulate crash/restart + del journal.current + + assert journal.has_not_completed("main") + assert not journal.has_not_completed("pre") + + +# need a real class so that it can be pickled later +class JournalledMemory(restart.Journalled): + # divide is a dummy protocol + protocols = ["divide", "multiply"] + + def __init__(self): + self.memory = 1 + super().__init__() + + def multiply(self, x): + self.journal.start("multiply") + self.memory *= x + self.journal.completed("multiply") + + +@pytest.fixture +def journalled(): + return JournalledMemory() + + +class TestJournalled: + @staticmethod + def divide(m, x): + return m.memory / x + + def test_get_protocol_of_class(self, journalled): + f = journalled.get_protocol("multiply") + f(10) + assert journalled.memory == 10 + assert journalled.journal.has_completed("multiply") + + def test_get_protocol_dummy(self, journalled): + dummy_protocol = journalled.get_protocol("divide") + result = dummy_protocol(self.divide, journalled, 10) + + assert result == 1 / 10 + assert journalled.journal.has_completed("divide") + + def test_get_protocol_dummy_incomplete(self, journalled): + dummy_protocol = journalled.get_protocol("divide") + with pytest.raises(ZeroDivisionError): + result = dummy_protocol(self.divide, journalled, 0) + assert not journalled.journal.has_completed("divide") + + def test_save_load(self, tmp_path): + # instantiate a class that can be pickled (without pytest magic) + journalled = JournalledMemory() + f = journalled.get_protocol("multiply") + f(10) + assert journalled.memory == 10 + + pickle = tmp_path / "memory.pkl" + journalled.save(pickle) + + assert pickle.exists() + + # change instance + f(99) + assert journalled.memory == 10 * 99 + + # reload previous state + journalled.load(pickle) + assert journalled.memory == 10 diff --git a/mdpow/tests/test_solvation.py b/mdpow/tests/test_solvation.py index d2d75404..56b99b73 100644 --- a/mdpow/tests/test_solvation.py +++ b/mdpow/tests/test_solvation.py @@ -1,5 +1,7 @@ import os import shutil +from pathlib import Path +from typing import Dict, Type from gromacs.utilities import in_dir import gromacs @@ -10,7 +12,7 @@ from . import RESOURCES -sims = { +sims: Dict[str, Type[equil.Simulation]] = { "water": equil.WaterSimulation, "octanol": equil.OctanolSimulation, "cyclohexane": equil.CyclohexaneSimulation, @@ -35,7 +37,7 @@ def setup(tmpdir): return newdir.dirname -def solvation(setup, solvent, ff="OPLS-AA"): +def solvation(setup: Path, solvent: str, ff="OPLS-AA"): itp = test_file[ff] with in_dir(setup, create=False): try: diff --git a/mdpow/workflows/dihedrals.py b/mdpow/workflows/dihedrals.py index 05e678a9..050cbd10 100644 --- a/mdpow/workflows/dihedrals.py +++ b/mdpow/workflows/dihedrals.py @@ -511,10 +511,12 @@ def periodic_angle_padding(df, padding=45): def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT, plot_title=None): """Plots kernel density estimates (KDE) of dihedral angle frequencies for one dihedral atom group as violin plots, using as input the augmented - :class:`pandas.DataFrame` from :func:`~mdpow.workflows.dihedrals.periodic_angle_padding`. + :class:`pandas.DataFrame` from + :func:`~mdpow.workflows.dihedrals.periodic_angle_padding`. Output is converted to SVG by :func:`~mdpow.workflows.dihedrals.build_svg` - and final output is saved as PDF by :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins` + and final output is saved as PDF by + :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins` :keywords: @@ -523,13 +525,13 @@ def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT, plot_title=None): :func:`~mdpow.workflows.dihedrals.periodic_angle_padding` *width* - width of the violin element (>1 overlaps) - default: 0.9 + width of the violin element (>1 overlaps); default: 0.9 *solvents* The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. + Normally takes a two-tuple, but analysis is compatible with single + solvent selections. Single solvent analyses will result in a figure + with fully filled violins for the single solvent. *plot_title* generated by :func:`~mdpow.workflows.dihedrals.build_svg` using @@ -619,9 +621,8 @@ def build_svg( solvents=SOLVENTS_DEFAULT, width=0.9, ): - """Converts and combines figure components into an - SVG object to be converted and saved as a publication - quality PDF. + """Converts and combines figure components into an SVG object to be + converted and saved as a publication quality PDF. :keywords: @@ -629,14 +630,13 @@ def build_svg( :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` *molname* - molecule name to be used for labelling - plots, if different from `resname` - (in this case, carried over from an upstream - decision between the two) + molecule name to be used for labelling plots, if different from + `resname` (in this case, carried over from an upstream decision between + the two) *name_index_pairs* - dictionary with key-value pair for dihedral atom group, - atom indices, and bond indices + dictionary with key-value pair for dihedral atom group, atom indices, + and bond indices .. seealso:: :func:`~mdpow.workflows.dihedrals.get_paired_indices` @@ -647,12 +647,12 @@ def build_svg( *solvents* The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. + Normally takes a two-tuple, but analysis is compatible with single + solvent selections. Single solvent analyses will result in a figure + with fully filled violins for the single solvent. *width* - width of the violin element (>1 overlaps) - default: 0.9 + width of the violin element (>1 overlaps); default: 0.9 :returns: diff --git a/setup.py b/setup.py index d6944529..32060d44 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,6 @@ # Copyright (c) 2010 Oliver Beckstein # Released under the GNU Public License 3 (or higher, your choice) -import sys from setuptools import setup, find_packages import versioneer @@ -27,9 +26,9 @@ "Operating System :: MacOS :: MacOS X", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Physics", ], @@ -47,6 +46,8 @@ "scripts/mdpow-solvationenergy", "scripts/mdpow-get-runinput", ], + # exclude large data sets in tests/testing_resources/* + include_package_data=True, package_data={ "mdpow": [ "top/*.dat", @@ -58,9 +59,14 @@ "templates/*", ], }, + exclude_package_data={ + "mdpow.tests": [ + "testing_resources/*", + ] + }, install_requires=[ "numpy>=1.6", - "scipy", + "scipy>=1.11.0", "pyyaml", "GromacsWrapper>=0.5.1", "numkit", @@ -77,6 +83,6 @@ "pypdf", ], # setup_requires=['pytest-runner',], - tests_require=["pytest", "pybol", "py"], + # tests_require=["pytest", "pybol", "py"], zip_safe=True, ) diff --git a/versioneer.py b/versioneer.py index 2b545405..de97d904 100644 --- a/versioneer.py +++ b/versioneer.py @@ -1,4 +1,4 @@ -# Version: 0.18 +# Version: 0.29 """The Versioneer - like a rocketeer, but for versions. @@ -6,18 +6,14 @@ ============== * like a rocketeer, but for versions! -* https://github.com/warner/python-versioneer +* https://github.com/python-versioneer/python-versioneer * Brian Warner -* License: Public Domain -* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy -* [![Latest Version] -(https://pypip.in/version/versioneer/badge.svg?style=flat) -](https://pypi.python.org/pypi/versioneer/) -* [![Build Status] -(https://travis-ci.org/warner/python-versioneer.png?branch=master) -](https://travis-ci.org/warner/python-versioneer) - -This is a tool for managing a recorded version number in distutils-based +* License: Public Domain (Unlicense) +* Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and pypy3 +* [![Latest Version][pypi-image]][pypi-url] +* [![Build Status][travis-image]][travis-url] + +This is a tool for managing a recorded version number in setuptools-based python projects. The goal is to remove the tedious and error-prone "update the embedded version string" step from your release process. Making a new release should be as easy as recording a new tag in your version-control @@ -26,9 +22,38 @@ ## Quick Install -* `pip install versioneer` to somewhere to your $PATH -* add a `[versioneer]` section to your setup.cfg (see below) -* run `versioneer install` in your source tree, commit the results +Versioneer provides two installation modes. The "classic" vendored mode installs +a copy of versioneer into your repository. The experimental build-time dependency mode +is intended to allow you to skip this step and simplify the process of upgrading. + +### Vendored mode + +* `pip install versioneer` to somewhere in your $PATH + * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is + available, so you can also use `conda install -c conda-forge versioneer` +* add a `[tool.versioneer]` section to your `pyproject.toml` or a + `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) + * Note that you will need to add `tomli; python_version < "3.11"` to your + build-time dependencies if you use `pyproject.toml` +* run `versioneer install --vendor` in your source tree, commit the results +* verify version information with `python setup.py version` + +### Build-time dependency mode + +* `pip install versioneer` to somewhere in your $PATH + * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is + available, so you can also use `conda install -c conda-forge versioneer` +* add a `[tool.versioneer]` section to your `pyproject.toml` or a + `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) +* add `versioneer` (with `[toml]` extra, if configuring in `pyproject.toml`) + to the `requires` key of the `build-system` table in `pyproject.toml`: + ```toml + [build-system] + requires = ["setuptools", "versioneer[toml]"] + build-backend = "setuptools.build_meta" + ``` +* run `versioneer install --no-vendor` in your source tree, commit the results +* verify version information with `python setup.py version` ## Version Identifiers @@ -60,7 +85,7 @@ for example `git describe --tags --dirty --always` reports things like "0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the 0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes. +uncommitted changes). The version identifier is used for multiple purposes: @@ -165,7 +190,7 @@ Some situations are known to cause problems for Versioneer. This details the most significant ones. More can be found on Github -[issues page](https://github.com/warner/python-versioneer/issues). +[issues page](https://github.com/python-versioneer/python-versioneer/issues). ### Subprojects @@ -179,7 +204,7 @@ `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI distributions (and upload multiple independently-installable tarballs). * Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other langauges) in subdirectories. + provide bindings to Python (and perhaps other languages) in subdirectories. Versioneer will look for `.git` in parent directories, and most operations should get the right version string. However `pip` and `setuptools` have bugs @@ -193,9 +218,9 @@ Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in some later version. -[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking +[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking this issue. The discussion in -[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the +[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the issue from the Versioneer side in more detail. [pip PR#3176](https://github.com/pypa/pip/pull/3176) and [pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve @@ -223,31 +248,20 @@ cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into a different virtualenv), so this can be surprising. -[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes +[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes this one, but upgrading to a newer version of setuptools should probably resolve it. -### Unicode version strings - -While Versioneer works (and is continually tested) with both Python 2 and -Python 3, it is not entirely consistent with bytes-vs-unicode distinctions. -Newer releases probably generate unicode version strings on py2. It's not -clear that this is wrong, but it may be surprising for applications when then -write these strings to a network connection or include them in bytes-oriented -APIs like cryptographic checksums. - -[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates -this question. - ## Updating Versioneer To upgrade your project to a new release of Versioneer, do the following: * install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg`, if necessary, to include any new configuration settings - indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install` in your source tree, to replace +* edit `setup.cfg` and `pyproject.toml`, if necessary, + to include any new configuration settings indicated by the release notes. + See [UPGRADING](./UPGRADING.md) for details. +* re-run `versioneer install --[no-]vendor` in your source tree, to replace `SRC/_version.py` * commit any changed files @@ -264,36 +278,70 @@ direction and include code from all supported VCS systems, reducing the number of intermediate scripts. +## Similar projects + +* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time + dependency +* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of + versioneer +* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools + plugin ## License To make Versioneer easier to embed, all its code is dedicated to the public domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . +Specifically, both are released under the "Unlicense", as described in +https://unlicense.org/. -""" +[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg +[pypi-url]: https://pypi.python.org/pypi/versioneer/ +[travis-image]: +https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg +[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer -from __future__ import print_function +""" +# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring +# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements +# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error +# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with +# pylint:disable=attribute-defined-outside-init,too-many-arguments -try: - import configparser -except ImportError: - import ConfigParser as configparser +import configparser import errno import json import os import re import subprocess import sys +from pathlib import Path +from typing import Any, Callable, cast, Dict, List, Optional, Tuple, Union +from typing import NoReturn +import functools + +have_tomllib = True +if sys.version_info >= (3, 11): + import tomllib +else: + try: + import tomli as tomllib + except ImportError: + have_tomllib = False class VersioneerConfig: """Container for Versioneer configuration parameters.""" + VCS: str + style: str + tag_prefix: str + versionfile_source: str + versionfile_build: Optional[str] + parentdir_prefix: Optional[str] + verbose: Optional[bool] + -def get_root(): +def get_root() -> str: """Get the project root directory. We require that all commands are run from the project root, i.e. the @@ -301,13 +349,23 @@ def get_root(): """ root = os.path.realpath(os.path.abspath(os.getcwd())) setup_py = os.path.join(root, "setup.py") + pyproject_toml = os.path.join(root, "pyproject.toml") versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): + if not ( + os.path.exists(setup_py) + or os.path.exists(pyproject_toml) + or os.path.exists(versioneer_py) + ): # allow 'python path/to/setup.py COMMAND' root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) setup_py = os.path.join(root, "setup.py") + pyproject_toml = os.path.join(root, "pyproject.toml") versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): + if not ( + os.path.exists(setup_py) + or os.path.exists(pyproject_toml) + or os.path.exists(versioneer_py) + ): err = ( "Versioneer was unable to run the project root directory. " "Versioneer requires setup.py to be executed from " @@ -323,46 +381,64 @@ def get_root(): # module-import table will cache the first one. So we can't use # os.path.dirname(__file__), as that will find whichever # versioneer.py was first imported, even in later projects. - me = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(me)[0]) + my_path = os.path.realpath(os.path.abspath(__file__)) + me_dir = os.path.normcase(os.path.splitext(my_path)[0]) vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir: + if me_dir != vsr_dir and "VERSIONEER_PEP518" not in globals(): print( "Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(me), versioneer_py) + % (os.path.dirname(my_path), versioneer_py) ) except NameError: pass return root -def get_config_from_root(root): +def get_config_from_root(root: str) -> VersioneerConfig: """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise EnvironmentError (if setup.cfg is missing), or + # This might raise OSError (if setup.cfg is missing), or # configparser.NoSectionError (if it lacks a [versioneer] section), or # configparser.NoOptionError (if it lacks "VCS="). See the docstring at # the top of versioneer.py for instructions on writing your setup.cfg . - setup_cfg = os.path.join(root, "setup.cfg") - parser = configparser.SafeConfigParser() - with open(setup_cfg, "r") as f: - parser.readfp(f) - VCS = parser.get("versioneer", "VCS") # mandatory - - def get(parser, name): - if parser.has_option("versioneer", name): - return parser.get("versioneer", name) - return None + root_pth = Path(root) + pyproject_toml = root_pth / "pyproject.toml" + setup_cfg = root_pth / "setup.cfg" + section: Union[Dict[str, Any], configparser.SectionProxy, None] = None + if pyproject_toml.exists() and have_tomllib: + try: + with open(pyproject_toml, "rb") as fobj: + pp = tomllib.load(fobj) + section = pp["tool"]["versioneer"] + except (tomllib.TOMLDecodeError, KeyError) as e: + print(f"Failed to load config from {pyproject_toml}: {e}") + print("Try to load it from setup.cfg") + if not section: + parser = configparser.ConfigParser() + with open(setup_cfg) as cfg_file: + parser.read_file(cfg_file) + parser.get("versioneer", "VCS") # raise error if missing + + section = parser["versioneer"] + + # `cast`` really shouldn't be used, but its simplest for the + # common VersioneerConfig users at the moment. We verify against + # `None` values elsewhere where it matters cfg = VersioneerConfig() - cfg.VCS = VCS - cfg.style = get(parser, "style") or "" - cfg.versionfile_source = get(parser, "versionfile_source") - cfg.versionfile_build = get(parser, "versionfile_build") - cfg.tag_prefix = get(parser, "tag_prefix") - if cfg.tag_prefix in ("''", '""'): + cfg.VCS = section["VCS"] + cfg.style = section.get("style", "") + cfg.versionfile_source = cast(str, section.get("versionfile_source")) + cfg.versionfile_build = section.get("versionfile_build") + cfg.tag_prefix = cast(str, section.get("tag_prefix")) + if cfg.tag_prefix in ("''", '""', None): cfg.tag_prefix = "" - cfg.parentdir_prefix = get(parser, "parentdir_prefix") - cfg.verbose = get(parser, "verbose") + cfg.parentdir_prefix = section.get("parentdir_prefix") + if isinstance(section, configparser.SectionProxy): + # Make sure configparser translates to bool + cfg.verbose = section.getboolean("verbose") + else: + cfg.verbose = section.get("verbose") + return cfg @@ -371,41 +447,54 @@ class NotThisMethod(Exception): # these dictionaries contain VCS-specific tools -LONG_VERSION_PY = {} -HANDLERS = {} +LONG_VERSION_PY: Dict[str, str] = {} +HANDLERS: Dict[str, Dict[str, Callable]] = {} -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" +def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator + """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): + def decorate(f: Callable) -> Callable: """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f + HANDLERS.setdefault(vcs, {})[method] = f return f return decorate -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): +def run_command( + commands: List[str], + args: List[str], + cwd: Optional[str] = None, + verbose: bool = False, + hide_stderr: bool = False, + env: Optional[Dict[str, str]] = None, +) -> Tuple[Optional[str], Optional[int]]: """Call the given command(s).""" assert isinstance(commands, list) - p = None - for c in commands: + process = None + + popen_kwargs: Dict[str, Any] = {} + if sys.platform == "win32": + # This hides the console window if pythonw.exe is used + startupinfo = subprocess.STARTUPINFO() + startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW + popen_kwargs["startupinfo"] = startupinfo + + for command in commands: try: - dispcmd = str([c] + args) + dispcmd = str([command] + args) # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen( - [c] + args, + process = subprocess.Popen( + [command] + args, cwd=cwd, env=env, stdout=subprocess.PIPE, stderr=(subprocess.PIPE if hide_stderr else None), + **popen_kwargs, ) break - except EnvironmentError: - e = sys.exc_info()[1] + except OSError as e: if e.errno == errno.ENOENT: continue if verbose: @@ -416,28 +505,27 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= if verbose: print("unable to find command, tried %s" % (commands,)) return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: + stdout = process.communicate()[0].strip().decode() + if process.returncode != 0: if verbose: print("unable to run %s (error)" % dispcmd) print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode + return None, process.returncode + return stdout, process.returncode LONG_VERSION_PY[ "git" -] = ''' +] = r''' # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build # directories (produced by setup.py build) will contain a much shorter file # that just contains the computed version number. -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) +# This file is released into the public domain. +# Generated by versioneer-0.29 +# https://github.com/python-versioneer/python-versioneer """Git implementation of _version.py.""" @@ -446,9 +534,11 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= import re import subprocess import sys +from typing import Any, Callable, Dict, List, Optional, Tuple +import functools -def get_keywords(): +def get_keywords() -> Dict[str, str]: """Get the keywords needed to look up the version information.""" # these strings will be replaced by git during git-archive. # setup.py/versioneer.py will grep for the variable names, so they must @@ -464,8 +554,15 @@ def get_keywords(): class VersioneerConfig: """Container for Versioneer configuration parameters.""" + VCS: str + style: str + tag_prefix: str + parentdir_prefix: str + versionfile_source: str + verbose: bool + -def get_config(): +def get_config() -> VersioneerConfig: """Create, populate and return the VersioneerConfig() object.""" # these strings are filled in when 'setup.py versioneer' creates # _version.py @@ -483,13 +580,13 @@ class NotThisMethod(Exception): """Exception raised if a method is not valid for the current scenario.""" -LONG_VERSION_PY = {} -HANDLERS = {} +LONG_VERSION_PY: Dict[str, str] = {} +HANDLERS: Dict[str, Dict[str, Callable]] = {} -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): +def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator + """Create decorator to mark a method as the handler of a VCS.""" + def decorate(f: Callable) -> Callable: """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} @@ -498,22 +595,35 @@ def decorate(f): return decorate -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): +def run_command( + commands: List[str], + args: List[str], + cwd: Optional[str] = None, + verbose: bool = False, + hide_stderr: bool = False, + env: Optional[Dict[str, str]] = None, +) -> Tuple[Optional[str], Optional[int]]: """Call the given command(s).""" assert isinstance(commands, list) - p = None - for c in commands: + process = None + + popen_kwargs: Dict[str, Any] = {} + if sys.platform == "win32": + # This hides the console window if pythonw.exe is used + startupinfo = subprocess.STARTUPINFO() + startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW + popen_kwargs["startupinfo"] = startupinfo + + for command in commands: try: - dispcmd = str([c] + args) + dispcmd = str([command] + args) # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) + process = subprocess.Popen([command] + args, cwd=cwd, env=env, + stdout=subprocess.PIPE, + stderr=(subprocess.PIPE if hide_stderr + else None), **popen_kwargs) break - except EnvironmentError: - e = sys.exc_info()[1] + except OSError as e: if e.errno == errno.ENOENT: continue if verbose: @@ -524,18 +634,20 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, if verbose: print("unable to find command, tried %%s" %% (commands,)) return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: + stdout = process.communicate()[0].strip().decode() + if process.returncode != 0: if verbose: print("unable to run %%s (error)" %% dispcmd) print("stdout was %%s" %% stdout) - return None, p.returncode - return stdout, p.returncode + return None, process.returncode + return stdout, process.returncode -def versions_from_parentdir(parentdir_prefix, root, verbose): +def versions_from_parentdir( + parentdir_prefix: str, + root: str, + verbose: bool, +) -> Dict[str, Any]: """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both @@ -544,15 +656,14 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): """ rootdirs = [] - for i in range(3): + for _ in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): return {"version": dirname[len(parentdir_prefix):], "full-revisionid": None, "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level + rootdirs.append(root) + root = os.path.dirname(root) # up a level if verbose: print("Tried directories %%s but none started with prefix %%s" %% @@ -561,41 +672,48 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): @register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): +def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. - keywords = {} + keywords: Dict[str, str] = {} try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: + with open(versionfile_abs, "r") as fobj: + for line in fobj: + if line.strip().startswith("git_refnames ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["refnames"] = mo.group(1) + if line.strip().startswith("git_full ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["full"] = mo.group(1) + if line.strip().startswith("git_date ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["date"] = mo.group(1) + except OSError: pass return keywords @register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): +def git_versions_from_keywords( + keywords: Dict[str, str], + tag_prefix: str, + verbose: bool, +) -> Dict[str, Any]: """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") + if "refnames" not in keywords: + raise NotThisMethod("Short version file found") date = keywords.get("date") if date is not None: + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] + # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 # -like" string, which we must then edit to make compliant), because @@ -608,11 +726,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) + refs = {r.strip() for r in refnames.strip("()").split(",")} # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) + tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %%d @@ -621,7 +739,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) + tags = {r for r in refs if re.search(r'\d', r)} if verbose: print("discarding '%%s', no digits" %% ",".join(refs - tags)) if verbose: @@ -630,6 +748,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): r = ref[len(tag_prefix):] + # Filter out refs that exactly match prefix or that don't start + # with a number once the prefix is stripped (mostly a concern + # when prefix is '') + if not re.match(r'\d', r): + continue if verbose: print("picking %%s" %% r) return {"version": r, @@ -645,7 +768,12 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): @register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): +def git_pieces_from_vcs( + tag_prefix: str, + root: str, + verbose: bool, + runner: Callable = run_command +) -> Dict[str, Any]: """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* @@ -656,8 +784,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) + # GIT_DIR can interfere with correct operation of Versioneer. + # It may be intended to be passed to the Versioneer-versioned project, + # but that should not change where we get our version from. + env = os.environ.copy() + env.pop("GIT_DIR", None) + runner = functools.partial(runner, env=env) + + _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, + hide_stderr=not verbose) if rc != 0: if verbose: print("Directory %%s not under git control" %% root) @@ -665,24 +800,57 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%%s*" %% tag_prefix], - cwd=root) + describe_out, rc = runner(GITS, [ + "describe", "--tags", "--dirty", "--always", "--long", + "--match", f"{tag_prefix}[[:digit:]]*" + ], cwd=root) # --long was added in git-1.5.5 if describe_out is None: raise NotThisMethod("'git describe' failed") describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) + full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) if full_out is None: raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() - pieces = {} + pieces: Dict[str, Any] = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None + branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], + cwd=root) + # --abbrev-ref was added in git-1.6.3 + if rc != 0 or branch_name is None: + raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") + branch_name = branch_name.strip() + + if branch_name == "HEAD": + # If we aren't exactly on a branch, pick a branch which represents + # the current commit. If all else fails, we are on a branchless + # commit. + branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) + # --contains was added in git-1.5.4 + if rc != 0 or branches is None: + raise NotThisMethod("'git branch --contains' returned error") + branches = branches.split("\n") + + # Remove the first line if we're running detached + if "(" in branches[0]: + branches.pop(0) + + # Strip off the leading "* " from the list of branches. + branches = [branch[2:] for branch in branches] + if "master" in branches: + branch_name = "master" + elif not branches: + branch_name = None + else: + # Pick the first branch that is returned. Good or bad. + branch_name = branches[0] + + pieces["branch"] = branch_name + # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] # TAG might have hyphens. git_describe = describe_out @@ -699,7 +867,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # TAG-NUM-gHEX mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) if not mo: - # unparseable. Maybe git-describe is misbehaving? + # unparsable. Maybe git-describe is misbehaving? pieces["error"] = ("unable to parse git-describe output: '%%s'" %% describe_out) return pieces @@ -724,26 +892,27 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): else: # HEX: no tags pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits + out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) + pieces["distance"] = len(out.split()) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"], - cwd=root)[0].strip() + date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip() + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces -def plus_or_dot(pieces): +def plus_or_dot(pieces: Dict[str, Any]) -> str: """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" -def render_pep440(pieces): +def render_pep440(pieces: Dict[str, Any]) -> str: """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you @@ -768,23 +937,71 @@ def render_pep440(pieces): return rendered -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. +def render_pep440_branch(pieces: Dict[str, Any]) -> str: + """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . + + The ".dev0" means not master branch. Note that .dev0 sorts backwards + (a feature branch will appear "older" than the master branch). Exceptions: - 1: no tags. 0.post.devDISTANCE + 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0" + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+untagged.%%d.g%%s" %% (pieces["distance"], + pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: + """Split pep440 version string at the post-release segment. + + Returns the release segments before the post-release and the + post-release version number (or -1 if no post-release segment is present). + """ + vc = str.split(ver, ".post") + return vc[0], int(vc[1] or 0) if len(vc) == 2 else None + + +def render_pep440_pre(pieces: Dict[str, Any]) -> str: + """TAG[.postN.devDISTANCE] -- No -dirty. + + Exceptions: + 1: no tags. 0.post0.devDISTANCE + """ + if pieces["closest-tag"]: if pieces["distance"]: - rendered += ".post.dev%%d" %% pieces["distance"] + # update the post release segment + tag_version, post_version = pep440_split_post(pieces["closest-tag"]) + rendered = tag_version + if post_version is not None: + rendered += ".post%%d.dev%%d" %% (post_version + 1, pieces["distance"]) + else: + rendered += ".post0.dev%%d" %% (pieces["distance"]) + else: + # no commits, use the tag as the version + rendered = pieces["closest-tag"] else: # exception #1 - rendered = "0.post.dev%%d" %% pieces["distance"] + rendered = "0.post0.dev%%d" %% pieces["distance"] return rendered -def render_pep440_post(pieces): +def render_pep440_post(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards @@ -811,12 +1028,41 @@ def render_pep440_post(pieces): return rendered -def render_pep440_old(pieces): +def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: + """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . + + The ".dev0" means not master branch. + + Exceptions: + 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + rendered += ".post%%d" %% pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "g%%s" %% pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0.post%%d" %% pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+g%%s" %% pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def render_pep440_old(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. - Eexceptions: + Exceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: @@ -833,7 +1079,7 @@ def render_pep440_old(pieces): return rendered -def render_git_describe(pieces): +def render_git_describe(pieces: Dict[str, Any]) -> str: """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. @@ -853,7 +1099,7 @@ def render_git_describe(pieces): return rendered -def render_git_describe_long(pieces): +def render_git_describe_long(pieces: Dict[str, Any]) -> str: """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. @@ -873,7 +1119,7 @@ def render_git_describe_long(pieces): return rendered -def render(pieces, style): +def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: """Render the given version pieces into the requested style.""" if pieces["error"]: return {"version": "unknown", @@ -887,10 +1133,14 @@ def render(pieces, style): if style == "pep440": rendered = render_pep440(pieces) + elif style == "pep440-branch": + rendered = render_pep440_branch(pieces) elif style == "pep440-pre": rendered = render_pep440_pre(pieces) elif style == "pep440-post": rendered = render_pep440_post(pieces) + elif style == "pep440-post-branch": + rendered = render_pep440_post_branch(pieces) elif style == "pep440-old": rendered = render_pep440_old(pieces) elif style == "git-describe": @@ -905,7 +1155,7 @@ def render(pieces, style): "date": pieces.get("date")} -def get_versions(): +def get_versions() -> Dict[str, Any]: """Get version information or return default if unable to do so.""" # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have # __file__, we can work backwards from there to the root. Some @@ -926,7 +1176,7 @@ def get_versions(): # versionfile_source is the relative path from the top of the source # tree (where the .git directory might live) to this file. Invert # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): + for _ in cfg.versionfile_source.split('/'): root = os.path.dirname(root) except NameError: return {"version": "0+unknown", "full-revisionid": None, @@ -953,41 +1203,48 @@ def get_versions(): @register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): +def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. - keywords = {} + keywords: Dict[str, str] = {} try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: + with open(versionfile_abs, "r") as fobj: + for line in fobj: + if line.strip().startswith("git_refnames ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["refnames"] = mo.group(1) + if line.strip().startswith("git_full ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["full"] = mo.group(1) + if line.strip().startswith("git_date ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["date"] = mo.group(1) + except OSError: pass return keywords @register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): +def git_versions_from_keywords( + keywords: Dict[str, str], + tag_prefix: str, + verbose: bool, +) -> Dict[str, Any]: """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") + if "refnames" not in keywords: + raise NotThisMethod("Short version file found") date = keywords.get("date") if date is not None: + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] + # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 # -like" string, which we must then edit to make compliant), because @@ -1000,11 +1257,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) + refs = {r.strip() for r in refnames.strip("()").split(",")} # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) + tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -1013,7 +1270,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r"\d", r)]) + tags = {r for r in refs if re.search(r"\d", r)} if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: @@ -1022,6 +1279,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): r = ref[len(tag_prefix) :] + # Filter out refs that exactly match prefix or that don't start + # with a number once the prefix is stripped (mostly a concern + # when prefix is '') + if not re.match(r"\d", r): + continue if verbose: print("picking %s" % r) return { @@ -1044,7 +1306,9 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): @register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): +def git_pieces_from_vcs( + tag_prefix: str, root: str, verbose: bool, runner: Callable = run_command +) -> Dict[str, Any]: """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* @@ -1055,7 +1319,14 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) + # GIT_DIR can interfere with correct operation of Versioneer. + # It may be intended to be passed to the Versioneer-versioned project, + # but that should not change where we get our version from. + env = os.environ.copy() + env.pop("GIT_DIR", None) + runner = functools.partial(runner, env=env) + + _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose) if rc != 0: if verbose: print("Directory %s not under git control" % root) @@ -1063,7 +1334,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command( + describe_out, rc = runner( GITS, [ "describe", @@ -1072,7 +1343,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): "--always", "--long", "--match", - "%s*" % tag_prefix, + f"{tag_prefix}[[:digit:]]*", ], cwd=root, ) @@ -1080,16 +1351,48 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if describe_out is None: raise NotThisMethod("'git describe' failed") describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) + full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) if full_out is None: raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() - pieces = {} + pieces: Dict[str, Any] = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None + branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root) + # --abbrev-ref was added in git-1.6.3 + if rc != 0 or branch_name is None: + raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") + branch_name = branch_name.strip() + + if branch_name == "HEAD": + # If we aren't exactly on a branch, pick a branch which represents + # the current commit. If all else fails, we are on a branchless + # commit. + branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) + # --contains was added in git-1.5.4 + if rc != 0 or branches is None: + raise NotThisMethod("'git branch --contains' returned error") + branches = branches.split("\n") + + # Remove the first line if we're running detached + if "(" in branches[0]: + branches.pop(0) + + # Strip off the leading "* " from the list of branches. + branches = [branch[2:] for branch in branches] + if "master" in branches: + branch_name = "master" + elif not branches: + branch_name = None + else: + # Pick the first branch that is returned. Good or bad. + branch_name = branches[0] + + pieces["branch"] = branch_name + # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] # TAG might have hyphens. git_describe = describe_out @@ -1106,7 +1409,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # TAG-NUM-gHEX mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) if not mo: - # unparseable. Maybe git-describe is misbehaving? + # unparsable. Maybe git-describe is misbehaving? pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out return pieces @@ -1132,19 +1435,20 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): else: # HEX: no tags pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) - pieces["distance"] = int(count_out) # total number of commits + out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) + pieces["distance"] = len(out.split()) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[ - 0 - ].strip() + date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces -def do_vcs_install(manifest_in, versionfile_source, ipy): +def do_vcs_install(versionfile_source: str, ipy: Optional[str]) -> None: """Git-specific installation logic for Versioneer. For Git, this means creating/changing .gitattributes to mark _version.py @@ -1153,36 +1457,40 @@ def do_vcs_install(manifest_in, versionfile_source, ipy): GITS = ["git"] if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - files = [manifest_in, versionfile_source] + files = [versionfile_source] if ipy: files.append(ipy) - try: - me = __file__ - if me.endswith(".pyc") or me.endswith(".pyo"): - me = os.path.splitext(me)[0] + ".py" - versioneer_file = os.path.relpath(me) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) + if "VERSIONEER_PEP518" not in globals(): + try: + my_path = __file__ + if my_path.endswith((".pyc", ".pyo")): + my_path = os.path.splitext(my_path)[0] + ".py" + versioneer_file = os.path.relpath(my_path) + except NameError: + versioneer_file = "versioneer.py" + files.append(versioneer_file) present = False try: - f = open(".gitattributes", "r") - for line in f.readlines(): - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - f.close() - except EnvironmentError: + with open(".gitattributes", "r") as fobj: + for line in fobj: + if line.strip().startswith(versionfile_source): + if "export-subst" in line.strip().split()[1:]: + present = True + break + except OSError: pass if not present: - f = open(".gitattributes", "a+") - f.write("%s export-subst\n" % versionfile_source) - f.close() + with open(".gitattributes", "a+") as fobj: + fobj.write(f"{versionfile_source} export-subst\n") files.append(".gitattributes") run_command(GITS, ["add", "--"] + files) -def versions_from_parentdir(parentdir_prefix, root, verbose): +def versions_from_parentdir( + parentdir_prefix: str, + root: str, + verbose: bool, +) -> Dict[str, Any]: """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both @@ -1191,7 +1499,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): """ rootdirs = [] - for i in range(3): + for _ in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): return { @@ -1201,9 +1509,8 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): "error": None, "date": None, } - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level + rootdirs.append(root) + root = os.path.dirname(root) # up a level if verbose: print( @@ -1214,7 +1521,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.18) from +# This file was generated by 'versioneer.py' (0.29) from # revision-control system data, or from the parent directory name of an # unpacked source archive. Distribution tarballs contain a pre-generated copy # of this file. @@ -1231,12 +1538,12 @@ def get_versions(): """ -def versions_from_file(filename): +def versions_from_file(filename: str) -> Dict[str, Any]: """Try to determine the version from _version.py if present.""" try: with open(filename) as f: contents = f.read() - except EnvironmentError: + except OSError: raise NotThisMethod("unable to read _version.py") mo = re.search( r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S @@ -1250,9 +1557,8 @@ def versions_from_file(filename): return json.loads(mo.group(1)) -def write_to_version_file(filename, versions): +def write_to_version_file(filename: str, versions: Dict[str, Any]) -> None: """Write the given version number to the given _version.py file.""" - os.unlink(filename) contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) with open(filename, "w") as f: f.write(SHORT_VERSION_PY % contents) @@ -1260,14 +1566,14 @@ def write_to_version_file(filename, versions): print("set %s to '%s'" % (filename, versions["version"])) -def plus_or_dot(pieces): +def plus_or_dot(pieces: Dict[str, Any]) -> str: """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" -def render_pep440(pieces): +def render_pep440(pieces: Dict[str, Any]) -> str: """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you @@ -1291,23 +1597,70 @@ def render_pep440(pieces): return rendered -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. +def render_pep440_branch(pieces: Dict[str, Any]) -> str: + """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . + + The ".dev0" means not master branch. Note that .dev0 sorts backwards + (a feature branch will appear "older" than the master branch). Exceptions: - 1: no tags. 0.post.devDISTANCE + 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0" + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: + """Split pep440 version string at the post-release segment. + + Returns the release segments before the post-release and the + post-release version number (or -1 if no post-release segment is present). + """ + vc = str.split(ver, ".post") + return vc[0], int(vc[1] or 0) if len(vc) == 2 else None + + +def render_pep440_pre(pieces: Dict[str, Any]) -> str: + """TAG[.postN.devDISTANCE] -- No -dirty. + + Exceptions: + 1: no tags. 0.post0.devDISTANCE + """ + if pieces["closest-tag"]: if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] + # update the post release segment + tag_version, post_version = pep440_split_post(pieces["closest-tag"]) + rendered = tag_version + if post_version is not None: + rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) + else: + rendered += ".post0.dev%d" % (pieces["distance"]) + else: + # no commits, use the tag as the version + rendered = pieces["closest-tag"] else: # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] + rendered = "0.post0.dev%d" % pieces["distance"] return rendered -def render_pep440_post(pieces): +def render_pep440_post(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards @@ -1334,12 +1687,41 @@ def render_pep440_post(pieces): return rendered -def render_pep440_old(pieces): +def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: + """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . + + The ".dev0" means not master branch. + + Exceptions: + 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + rendered += ".post%d" % pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "g%s" % pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0.post%d" % pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+g%s" % pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def render_pep440_old(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. - Eexceptions: + Exceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: @@ -1356,7 +1738,7 @@ def render_pep440_old(pieces): return rendered -def render_git_describe(pieces): +def render_git_describe(pieces: Dict[str, Any]) -> str: """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. @@ -1376,7 +1758,7 @@ def render_git_describe(pieces): return rendered -def render_git_describe_long(pieces): +def render_git_describe_long(pieces: Dict[str, Any]) -> str: """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. @@ -1396,7 +1778,7 @@ def render_git_describe_long(pieces): return rendered -def render(pieces, style): +def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: """Render the given version pieces into the requested style.""" if pieces["error"]: return { @@ -1412,10 +1794,14 @@ def render(pieces, style): if style == "pep440": rendered = render_pep440(pieces) + elif style == "pep440-branch": + rendered = render_pep440_branch(pieces) elif style == "pep440-pre": rendered = render_pep440_pre(pieces) elif style == "pep440-post": rendered = render_pep440_post(pieces) + elif style == "pep440-post-branch": + rendered = render_pep440_post_branch(pieces) elif style == "pep440-old": rendered = render_pep440_old(pieces) elif style == "git-describe": @@ -1438,7 +1824,7 @@ class VersioneerBadRootError(Exception): """The project root directory is unknown or missing key files.""" -def get_versions(verbose=False): +def get_versions(verbose: bool = False) -> Dict[str, Any]: """Get the project version from whatever source is available. Returns dict with two keys: 'version' and 'full'. @@ -1453,7 +1839,7 @@ def get_versions(verbose=False): assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" handlers = HANDLERS.get(cfg.VCS) assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose + verbose = verbose or bool(cfg.verbose) # `bool()` used to avoid `None` assert ( cfg.versionfile_source is not None ), "please set versioneer.versionfile_source" @@ -1519,13 +1905,17 @@ def get_versions(verbose=False): } -def get_version(): +def get_version() -> str: """Get the short version string for this project.""" return get_versions()["version"] -def get_cmdclass(): - """Get the custom setuptools/distutils subclasses used by Versioneer.""" +def get_cmdclass(cmdclass: Optional[Dict[str, Any]] = None): + """Get the custom setuptools subclasses used by Versioneer. + + If the package uses a different cmdclass (e.g. one from numpy), it + should be provide as an argument. + """ if "versioneer" in sys.modules: del sys.modules["versioneer"] # this fixes the "python setup.py develop" case (also 'install' and @@ -1539,25 +1929,25 @@ def get_cmdclass(): # parent is protected against the child's "import versioneer". By # removing ourselves from sys.modules here, before the child build # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/warner/python-versioneer/issues/52 + # Also see https://github.com/python-versioneer/python-versioneer/issues/52 - cmds = {} + cmds = {} if cmdclass is None else cmdclass.copy() - # we add "version" to both distutils and setuptools - from distutils.core import Command + # we add "version" to setuptools + from setuptools import Command class cmd_version(Command): description = "report generated version string" - user_options = [] - boolean_options = [] + user_options: List[Tuple[str, str, str]] = [] + boolean_options: List[str] = [] - def initialize_options(self): + def initialize_options(self) -> None: pass - def finalize_options(self): + def finalize_options(self) -> None: pass - def run(self): + def run(self) -> None: vers = get_versions(verbose=True) print("Version: %s" % vers["version"]) print(" full-revisionid: %s" % vers.get("full-revisionid")) @@ -1568,7 +1958,7 @@ def run(self): cmds["version"] = cmd_version - # we override "build_py" in both distutils and setuptools + # we override "build_py" in setuptools # # most invocation pathways end up running build_py: # distutils/build -> build_py @@ -1583,18 +1973,25 @@ def run(self): # then does setup.py bdist_wheel, or sometimes setup.py install # setup.py egg_info -> ? + # pip install -e . and setuptool/editable_wheel will invoke build_py + # but the build_py command is not expected to copy any files. + # we override different "build_py" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.build_py import build_py as _build_py + if "build_py" in cmds: + _build_py: Any = cmds["build_py"] else: - from distutils.command.build_py import build_py as _build_py + from setuptools.command.build_py import build_py as _build_py class cmd_build_py(_build_py): - def run(self): + def run(self) -> None: root = get_root() cfg = get_config_from_root(root) versions = get_versions() _build_py.run(self) + if getattr(self, "editable_mode", False): + # During editable installs `.py` and data files are + # not copied to build_lib + return # now locate _version.py in the new build/ directory and replace # it with an updated value if cfg.versionfile_build: @@ -1604,8 +2001,42 @@ def run(self): cmds["build_py"] = cmd_build_py + if "build_ext" in cmds: + _build_ext: Any = cmds["build_ext"] + else: + from setuptools.command.build_ext import build_ext as _build_ext + + class cmd_build_ext(_build_ext): + def run(self) -> None: + root = get_root() + cfg = get_config_from_root(root) + versions = get_versions() + _build_ext.run(self) + if self.inplace: + # build_ext --inplace will only build extensions in + # build/lib<..> dir with no _version.py to write to. + # As in place builds will already have a _version.py + # in the module dir, we do not need to write one. + return + # now locate _version.py in the new build/ directory and replace + # it with an updated value + if not cfg.versionfile_build: + return + target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) + if not os.path.exists(target_versionfile): + print( + f"Warning: {target_versionfile} does not exist, skipping " + "version update. This can happen if you are running build_ext " + "without first running build_py." + ) + return + print("UPDATING %s" % target_versionfile) + write_to_version_file(target_versionfile, versions) + + cmds["build_ext"] = cmd_build_ext + if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe + from cx_Freeze.dist import build_exe as _build_exe # type: ignore # nczeczulin reports that py2exe won't like the pep440-style string # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. @@ -1615,7 +2046,7 @@ def run(self): # ... class cmd_build_exe(_build_exe): - def run(self): + def run(self) -> None: root = get_root() cfg = get_config_from_root(root) versions = get_versions() @@ -1643,12 +2074,12 @@ def run(self): if "py2exe" in sys.modules: # py2exe enabled? try: - from py2exe.distutils_buildexe import py2exe as _py2exe # py3 + from py2exe.setuptools_buildexe import py2exe as _py2exe # type: ignore except ImportError: - from py2exe.build_exe import py2exe as _py2exe # py2 + from py2exe.distutils_buildexe import py2exe as _py2exe # type: ignore class cmd_py2exe(_py2exe): - def run(self): + def run(self) -> None: root = get_root() cfg = get_config_from_root(root) versions = get_versions() @@ -1673,14 +2104,54 @@ def run(self): cmds["py2exe"] = cmd_py2exe + # sdist farms its file list building out to egg_info + if "egg_info" in cmds: + _egg_info: Any = cmds["egg_info"] + else: + from setuptools.command.egg_info import egg_info as _egg_info + + class cmd_egg_info(_egg_info): + def find_sources(self) -> None: + # egg_info.find_sources builds the manifest list and writes it + # in one shot + super().find_sources() + + # Modify the filelist and normalize it + root = get_root() + cfg = get_config_from_root(root) + self.filelist.append("versioneer.py") + if cfg.versionfile_source: + # There are rare cases where versionfile_source might not be + # included by default, so we must be explicit + self.filelist.append(cfg.versionfile_source) + self.filelist.sort() + self.filelist.remove_duplicates() + + # The write method is hidden in the manifest_maker instance that + # generated the filelist and was thrown away + # We will instead replicate their final normalization (to unicode, + # and POSIX-style paths) + from setuptools import unicode_utils + + normalized = [ + unicode_utils.filesys_decode(f).replace(os.sep, "/") + for f in self.filelist.files + ] + + manifest_filename = os.path.join(self.egg_info, "SOURCES.txt") + with open(manifest_filename, "w") as fobj: + fobj.write("\n".join(normalized)) + + cmds["egg_info"] = cmd_egg_info + # we override different "sdist" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.sdist import sdist as _sdist + if "sdist" in cmds: + _sdist: Any = cmds["sdist"] else: - from distutils.command.sdist import sdist as _sdist + from setuptools.command.sdist import sdist as _sdist class cmd_sdist(_sdist): - def run(self): + def run(self) -> None: versions = get_versions() self._versioneer_generated_versions = versions # unless we update this, the command will keep using the old @@ -1688,7 +2159,7 @@ def run(self): self.distribution.metadata.version = versions["version"] return _sdist.run(self) - def make_release_tree(self, base_dir, files): + def make_release_tree(self, base_dir: str, files: List[str]) -> None: root = get_root() cfg = get_config_from_root(root) _sdist.make_release_tree(self, base_dir, files) @@ -1743,24 +2214,25 @@ def make_release_tree(self, base_dir, files): """ -INIT_PY_SNIPPET = """ +OLD_SNIPPET = """ from ._version import get_versions __version__ = get_versions()['version'] del get_versions """ +INIT_PY_SNIPPET = """ +from . import {0} +__version__ = {0}.get_versions()['version'] +""" + -def do_setup(): - """Main VCS-independent setup function for installing Versioneer.""" +def do_setup() -> int: + """Do main VCS-independent setup function for installing Versioneer.""" root = get_root() try: cfg = get_config_from_root(root) - except ( - EnvironmentError, - configparser.NoSectionError, - configparser.NoOptionError, - ) as e: - if isinstance(e, (EnvironmentError, configparser.NoSectionError)): + except (OSError, configparser.NoSectionError, configparser.NoOptionError) as e: + if isinstance(e, (OSError, configparser.NoSectionError)): print("Adding sample versioneer config to setup.cfg", file=sys.stderr) with open(os.path.join(root, "setup.cfg"), "a") as f: f.write(SAMPLE_CONFIG) @@ -1782,64 +2254,37 @@ def do_setup(): ) ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") + maybe_ipy: Optional[str] = ipy if os.path.exists(ipy): try: with open(ipy, "r") as f: old = f.read() - except EnvironmentError: + except OSError: old = "" - if INIT_PY_SNIPPET not in old: + module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0] + snippet = INIT_PY_SNIPPET.format(module) + if OLD_SNIPPET in old: + print(" replacing boilerplate in %s" % ipy) + with open(ipy, "w") as f: + f.write(old.replace(OLD_SNIPPET, snippet)) + elif snippet not in old: print(" appending to %s" % ipy) with open(ipy, "a") as f: - f.write(INIT_PY_SNIPPET) + f.write(snippet) else: print(" %s unmodified" % ipy) else: print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make sure both the top-level "versioneer.py" and versionfile_source - # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so - # they'll be copied into source distributions. Pip won't be able to - # install the package without this. - manifest_in = os.path.join(root, "MANIFEST.in") - simple_includes = set() - try: - with open(manifest_in, "r") as f: - for line in f: - if line.startswith("include "): - for include in line.split()[1:]: - simple_includes.add(include) - except EnvironmentError: - pass - # That doesn't cover everything MANIFEST.in can do - # (http://docs.python.org/2/distutils/sourcedist.html#commands), so - # it might give some false negatives. Appending redundant 'include' - # lines is safe, though. - if "versioneer.py" not in simple_includes: - print(" appending 'versioneer.py' to MANIFEST.in") - with open(manifest_in, "a") as f: - f.write("include versioneer.py\n") - else: - print(" 'versioneer.py' already in MANIFEST.in") - if cfg.versionfile_source not in simple_includes: - print( - " appending versionfile_source ('%s') to MANIFEST.in" - % cfg.versionfile_source - ) - with open(manifest_in, "a") as f: - f.write("include %s\n" % cfg.versionfile_source) - else: - print(" versionfile_source already in MANIFEST.in") + maybe_ipy = None # Make VCS-specific changes. For git, this means creating/changing # .gitattributes to mark _version.py for export-subst keyword # substitution. - do_vcs_install(manifest_in, cfg.versionfile_source, ipy) + do_vcs_install(cfg.versionfile_source, maybe_ipy) return 0 -def scan_setup_py(): +def scan_setup_py() -> int: """Validate the contents of setup.py against Versioneer's expectations.""" found = set() setters = False @@ -1876,10 +2321,14 @@ def scan_setup_py(): return errors +def setup_command() -> NoReturn: + """Set up Versioneer and exit with appropriate error code.""" + errors = do_setup() + errors += scan_setup_py() + sys.exit(1 if errors else 0) + + if __name__ == "__main__": cmd = sys.argv[1] if cmd == "setup": - errors = do_setup() - errors += scan_setup_py() - if errors: - sys.exit(1) + setup_command()