From 16ef76229bb2e6cda1fadc7959e8b94fae77f240 Mon Sep 17 00:00:00 2001 From: CalCraven Date: Sun, 22 Oct 2023 21:16:02 -0500 Subject: [PATCH] Skeleton of README details --- README.md | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/README.md b/README.md index da5fd9d..ab9b052 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,43 @@ # MoSDeF-dihedral-fit MoSDeF-dihedral-fit: A simple software package to fit dihedrals via the MoSDeF software + +This package is a tool to add dihedral parameters for [Ryckaert-Bellemans](https://manual.gromacs.org/current/reference-manual/functions/bonded-interactions.html#proper-dihedrals-ryckaert-bellemans-function) dihedral based forcefields by fitting QM calculations for the rotation about the dihedral angle to this functional form. The main functionality is found through the following code snippet. +```python +>>> import unyt as u +>>> from mosdef_dihedral_fit.dihedral_fit.fit_dihedral_with_gomc import fit_dihedral_with_gomc +>>> fit_dihedral_with_gomc( + ["HC", "CT", "CT", "HC"], + "molecule.mol2" + "compound.xml", + 298.15 * u.Kelvin, + gomc_binary_directory, + {"HC_CT_CT_HC_multiplicity_1.log": []}, + zeroed_dihedral_atom_types=None, + qm_engine="gaussian", + VDWGeometricSigma=False, + atom_type_naming_style="general", + gomc_cpu_cores=1, + fit_min_validated_r_squared=0.99, + fit_validation_r_squared_rtol=1e-03, + ) +>>> import os +>>> os.system("cat RB_torsion_k_constants_fit_energy.txt") +``` + +## Installation/Setup +``` +conda install -c conda-forge mosdef_dihedral_fit +git clone https://github.com/GOMC-WSU/GOMC.git +cd GOMC +chmod u+x metamake.sh +./metamake.sh +./GOMC__XXXX +p4 in.conf # set to 4 threads +pytest -v +``` + +## Documentation + +## Examples +Some basic workflows that use this package + - [ethane dihedral](https://github.com/GOMC-WSU/GOMC_Examples/tree/main/MoSDeF-dihedral-fit/ethane_HC_CT_CT_HC) + - [propanoic acid dihedral](https://github.com/GOMC-WSU/GOMC_Examples/tree/main/MoSDeF-dihedral-fit/protonated_fragment_CT_CT_C_OH)