From b612bbbe8014f92ecbf411ab22fb0ad0895dc16e Mon Sep 17 00:00:00 2001 From: Ellen Zhong Date: Sun, 22 Jun 2014 05:48:58 -0400 Subject: [PATCH] removed unnecessary input files --- .../Gromacs/UnitTest/angle1/confout.gro | 12 - .../UnitTest/angle1/gromacs_stderr.txt | 112 ----- .../UnitTest/angle1/gromacs_stdout.txt | 8 - testing/inputs/Gromacs/UnitTest/angle1/md.log | 401 ------------------ .../inputs/Gromacs/UnitTest/angle1/mdout.mdp | 343 --------------- .../inputs/Gromacs/UnitTest/angle1/topol.tpr | Bin 4312 -> 0 bytes .../Gromacs/UnitTest/angle2/confout.gro | 12 - .../UnitTest/angle2/gromacs_stderr.txt | 112 ----- .../UnitTest/angle2/gromacs_stdout.txt | 8 - testing/inputs/Gromacs/UnitTest/angle2/md.log | 401 ------------------ .../inputs/Gromacs/UnitTest/angle2/mdout.mdp | 343 --------------- .../inputs/Gromacs/UnitTest/angle2/topol.tpr | Bin 4312 -> 0 bytes .../Gromacs/UnitTest/angle3/confout.gro | 12 - .../UnitTest/angle3/gromacs_stderr.txt | 112 ----- .../UnitTest/angle3/gromacs_stdout.txt | 8 - testing/inputs/Gromacs/UnitTest/angle3/md.log | 401 ------------------ .../inputs/Gromacs/UnitTest/angle3/mdout.mdp | 343 --------------- .../inputs/Gromacs/UnitTest/angle3/topol.tpr | Bin 4292 -> 0 bytes .../Gromacs/UnitTest/angle4/confout.gro | 12 - .../UnitTest/angle4/gromacs_stderr.txt | 112 ----- .../UnitTest/angle4/gromacs_stdout.txt | 8 - testing/inputs/Gromacs/UnitTest/angle4/md.log | 401 ------------------ .../inputs/Gromacs/UnitTest/angle4/mdout.mdp | 343 --------------- .../inputs/Gromacs/UnitTest/angle4/topol.tpr | Bin 4312 -> 0 bytes .../Gromacs/UnitTest/angle5/confout.gro | 12 - .../UnitTest/angle5/gromacs_stderr.txt | 112 ----- .../UnitTest/angle5/gromacs_stdout.txt | 8 - testing/inputs/Gromacs/UnitTest/angle5/md.log | 401 ------------------ .../inputs/Gromacs/UnitTest/angle5/mdout.mdp | 343 --------------- .../inputs/Gromacs/UnitTest/angle5/topol.tpr | Bin 4392 -> 0 bytes .../Gromacs/UnitTest/angle6/confout.gro | 12 - .../UnitTest/angle6/gromacs_stderr.txt | 112 ----- .../UnitTest/angle6/gromacs_stdout.txt | 8 - testing/inputs/Gromacs/UnitTest/angle6/md.log | 401 ------------------ .../inputs/Gromacs/UnitTest/angle6/mdout.mdp | 343 --------------- .../inputs/Gromacs/UnitTest/angle6/topol.tpr | Bin 4352 -> 0 bytes .../inputs/Gromacs/UnitTest/bond1/confout.gro | 12 - .../Gromacs/UnitTest/bond1/gromacs_stderr.txt | 112 ----- .../Gromacs/UnitTest/bond1/gromacs_stdout.txt | 8 - testing/inputs/Gromacs/UnitTest/bond1/md.log | 401 ------------------ .../inputs/Gromacs/UnitTest/bond1/mdout.mdp | 343 --------------- .../inputs/Gromacs/UnitTest/bond1/topol.tpr | Bin 4312 -> 0 bytes .../inputs/Gromacs/UnitTest/bond2/confout.gro | 12 - .../Gromacs/UnitTest/bond2/gromacs_stderr.txt | 112 ----- .../Gromacs/UnitTest/bond2/gromacs_stdout.txt | 8 - testing/inputs/Gromacs/UnitTest/bond2/md.log | 401 ------------------ .../inputs/Gromacs/UnitTest/bond2/mdout.mdp | 343 --------------- 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.../Gromacs/UnitTest/bond6/gromacs_stderr.txt | 112 ----- .../Gromacs/UnitTest/bond6/gromacs_stdout.txt | 8 - .../inputs/Gromacs/UnitTest/bond6/mdout.mdp | 343 --------------- .../inputs/Gromacs/UnitTest/bond6/topol.tpr | Bin 4048 -> 0 bytes .../Gromacs/UnitTest/bond7/gromacs_stderr.txt | 103 ----- .../Gromacs/UnitTest/bond7/gromacs_stdout.txt | 8 - .../inputs/Gromacs/UnitTest/bond7/mdout.mdp | 343 --------------- .../inputs/Gromacs/UnitTest/bond7/topol.tpr | Bin 4280 -> 0 bytes .../Gromacs/UnitTest/dihedral1/confout.gro | 12 - .../UnitTest/dihedral1/gromacs_stderr.txt | 113 ----- .../UnitTest/dihedral1/gromacs_stdout.txt | 8 - .../inputs/Gromacs/UnitTest/dihedral1/md.log | 401 ------------------ .../Gromacs/UnitTest/dihedral1/mdout.mdp | 343 --------------- .../Gromacs/UnitTest/dihedral1/topol.tpr | Bin 4128 -> 0 bytes .../Gromacs/UnitTest/dihedral2/confout.gro | 12 - .../UnitTest/dihedral2/gromacs_stderr.txt | 113 ----- .../UnitTest/dihedral2/gromacs_stdout.txt | 8 - .../inputs/Gromacs/UnitTest/dihedral2/md.log | 401 ------------------ .../Gromacs/UnitTest/dihedral2/mdout.mdp | 343 --------------- .../Gromacs/UnitTest/dihedral2/topol.tpr | Bin 4124 -> 0 bytes .../Gromacs/UnitTest/dihedral3/confout.gro | 12 - .../UnitTest/dihedral3/gromacs_stderr.txt | 113 ----- .../UnitTest/dihedral3/gromacs_stdout.txt | 8 - .../inputs/Gromacs/UnitTest/dihedral3/md.log | 401 ------------------ .../Gromacs/UnitTest/dihedral3/mdout.mdp | 343 --------------- .../Gromacs/UnitTest/dihedral3/topol.tpr | Bin 4312 -> 0 bytes .../Gromacs/UnitTest/dihedral4/confout.gro | 12 - .../UnitTest/dihedral4/gromacs_stderr.txt | 113 ----- .../UnitTest/dihedral4/gromacs_stdout.txt | 8 - .../inputs/Gromacs/UnitTest/dihedral4/md.log | 401 ------------------ .../Gromacs/UnitTest/dihedral4/mdout.mdp | 343 --------------- .../Gromacs/UnitTest/dihedral4/topol.tpr | Bin 4128 -> 0 bytes .../Gromacs/UnitTest/dihedral5/confout.gro | 12 - .../UnitTest/dihedral5/gromacs_stderr.txt | 113 ----- 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testing/inputs/Gromacs/UnitTest/dihedral9/confout.gro delete mode 100644 testing/inputs/Gromacs/UnitTest/dihedral9/gromacs_stderr.txt delete mode 100644 testing/inputs/Gromacs/UnitTest/dihedral9/gromacs_stdout.txt delete mode 100644 testing/inputs/Gromacs/UnitTest/dihedral9/md.log delete mode 100644 testing/inputs/Gromacs/UnitTest/dihedral9/mdout.mdp delete mode 100644 testing/inputs/Gromacs/UnitTest/dihedral9/topol.tpr diff --git a/testing/inputs/Gromacs/UnitTest/angle1/confout.gro b/testing/inputs/Gromacs/UnitTest/angle1/confout.gro deleted file mode 100644 index e42c8e99..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle1/confout.gro +++ /dev/null @@ -1,12 +0,0 @@ -Ethanol - 9 - 1ETH CB 1 2.711 2.946 2.803 0.1006 -0.3737 0.2468 - 1ETH HB1 2 2.709 2.847 2.757 1.3518 3.0856 0.8708 - 1ETH HB2 3 2.616 2.954 2.855 -0.6358 -0.5466 -0.9490 - 1ETH OG1 4 2.804 2.957 2.907 0.1840 -0.1568 0.3435 - 1ETH HG1 5 2.883 2.946 2.857 -2.3209 0.8242 1.1101 - 1ETH CG2 6 2.732 3.048 2.687 -0.1720 0.3703 -0.4977 - 1ETH HG21 7 2.833 3.064 2.649 -1.9416 -0.3611 0.1548 - 1ETH HG22 8 2.700 3.145 2.723 2.1709 -0.9620 -3.0497 - 1ETH HG23 9 2.663 3.035 2.603 -0.6942 0.4885 -0.5993 - 3.01061 3.01061 3.01061 diff --git a/testing/inputs/Gromacs/UnitTest/angle1/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/angle1/gromacs_stderr.txt deleted file mode 100644 index 6d669821..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle1/gromacs_stderr.txt +++ /dev/null @@ -1,112 +0,0 @@ - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/angle1/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/angle1/angle1.gro Input Structure - file: gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/angle1/angle1.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/angle1/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/angle1/mdout.mdp to ./inputs/Gromacs/UnitTest/angle1/#mdout.mdp.26# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K - -WARNING 1 [file angle1.top, line 112]: - The bond in molecule-type Ethanol between atoms 4 OG1 and 5 HG1 has an - estimated oscillational period of 9.0e-03 ps, which is less than 5 times - the time step of 2.0e-03 ps. - Maybe you forgot to change the constraints mdp option. - -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -There was 1 warning - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/angle1/topol.tpr to ./inputs/Gromacs/UnitTest/angle1/#topol.tpr.26# - -gcq#42: "May the Force Be With You" (Star Wars) - diff --git a/testing/inputs/Gromacs/UnitTest/angle1/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/angle1/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle1/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/angle1/md.log b/testing/inputs/Gromacs/UnitTest/angle1/md.log deleted file mode 100644 index 75752be7..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle1/md.log +++ /dev/null @@ -1,401 +0,0 @@ -Log file opened on Fri Jun 20 15:51:39 2014 -Host: Christophs-MacBook-Air.local pid: 23206 nodeid: 0 nnodes: 1 -Gromacs version: VERSION 4.6.3 -Precision: single -Memory model: 64 bit -MPI library: thread_mpi -OpenMP support: disabled -GPU support: disabled -invsqrt routine: gmx_software_invsqrt(x) -CPU acceleration: AVX_256 -FFT library: fftw-3.3.2-sse2 -Large file support: enabled -RDTSCP usage: enabled -Built on: Tue Nov 19 15:39:55 CST 2013 -Built by: CTK@vpn-user-1-38.itc.virginia.edu [CMAKE] -Build OS/arch: Darwin 13.0.0 x86_64 -Build CPU vendor: GenuineIntel -Build CPU brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Build CPU family: 6 Model: 58 Stepping: 9 -Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -C compiler: /usr/bin/gcc Clang Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1 -C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG - - - :-) G R O M A C S (-: - - Great Red Oystrich Makes All Chemists Sane - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) mdrun (-: - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl -GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable -molecular simulation -J. Chem. Theory Comput. 4 (2008) pp. 435-447 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. -Berendsen -GROMACS: Fast, Flexible and Free -J. Comp. Chem. 26 (2005) pp. 1701-1719 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -E. Lindahl and B. Hess and D. van der Spoel -GROMACS 3.0: A package for molecular simulation and trajectory analysis -J. Mol. Mod. 7 (2001) pp. 306-317 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, D. van der Spoel and R. van Drunen -GROMACS: A message-passing parallel molecular dynamics implementation -Comp. Phys. Comm. 91 (1995) pp. 43-56 --------- -------- --- Thank You --- -------- -------- - -Input Parameters: - integrator = md-vv - nsteps = 0 - init-step = 0 - cutoff-scheme = Group - ns_type = Grid - nstlist = 10 - ndelta = 2 - nstcomm = 10 - comm-mode = Linear - nstlog = 1000 - nstxout = 1000 - nstvout = 1000 - nstfout = 0 - nstcalcenergy = 10 - nstenergy = 1000 - nstxtcout = 0 - init-t = 0 - delta-t = 0.002 - xtcprec = 1000 - fourierspacing = 0.12 - nkx = 28 - nky = 28 - nkz = 28 - pme-order = 4 - ewald-rtol = 1e-06 - ewald-geometry = 0 - epsilon-surface = 0 - optimize-fft = FALSE - ePBC = xyz - bPeriodicMols = FALSE - bContinuation = FALSE - bShakeSOR = FALSE - etc = Berendsen - bPrintNHChains = FALSE - nsttcouple = 1 - epc = Berendsen - epctype = Isotropic - nstpcouple = 1 - tau-p = 10 - ref-p (3x3): - ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} - ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} - ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} - compress (3x3): - compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} - compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} - compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} - refcoord-scaling = No - posres-com (3): - posres-com[0]= 0.00000e+00 - posres-com[1]= 0.00000e+00 - posres-com[2]= 0.00000e+00 - posres-comB (3): - posres-comB[0]= 0.00000e+00 - posres-comB[1]= 0.00000e+00 - posres-comB[2]= 0.00000e+00 - verlet-buffer-drift = 0.005 - rlist = 1.5 - rlistlong = 1.5 - nstcalclr = 0 - rtpi = 0.05 - coulombtype = PME - coulomb-modifier = None - rcoulomb-switch = 0 - rcoulomb = 1.5 - vdwtype = Switch - vdw-modifier = None - rvdw-switch = 1.2 - rvdw = 1.25 - epsilon-r = 1 - epsilon-rf = inf - tabext = 1 - implicit-solvent = No - gb-algorithm = Still - gb-epsilon-solvent = 80 - nstgbradii = 1 - rgbradii = 1 - gb-saltconc = 0 - gb-obc-alpha = 1 - gb-obc-beta = 0.8 - gb-obc-gamma = 4.85 - gb-dielectric-offset = 0.009 - sa-algorithm = Ace-approximation - sa-surface-tension = 2.05016 - DispCorr = AllEnerPres - bSimTemp = FALSE - free-energy = no - nwall = 0 - wall-type = 9-3 - wall-atomtype[0] = -1 - wall-atomtype[1] = -1 - wall-density[0] = 0 - wall-density[1] = 0 - wall-ewald-zfac = 3 - pull = no - rotation = FALSE - disre = No - disre-weighting = Conservative - disre-mixed = FALSE - dr-fc = 1000 - dr-tau = 0 - nstdisreout = 100 - orires-fc = 0 - orires-tau = 0 - nstorireout = 100 - dihre-fc = 0 - em-stepsize = 0.01 - em-tol = 10 - niter = 20 - fc-stepsize = 0 - nstcgsteep = 1000 - nbfgscorr = 10 - ConstAlg = Lincs - shake-tol = 0.0001 - lincs-order = 4 - lincs-warnangle = 30 - lincs-iter = 1 - bd-fric = 0 - ld-seed = 1993 - cos-accel = 0 - deform (3x3): - deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - adress = FALSE - userint1 = 0 - userint2 = 0 - userint3 = 0 - userint4 = 0 - userreal1 = 0 - userreal2 = 0 - userreal3 = 0 - userreal4 = 0 -grpopts: - nrdf: 24 - ref-t: 300 - tau-t: 10 -anneal: No -ann-npoints: 0 - acc: 0 0 0 - nfreeze: N N N - energygrp-flags[ 0]: 0 - efield-x: - n = 0 - efield-xt: - n = 0 - efield-y: - n = 0 - efield-yt: - n = 0 - efield-z: - n = 0 - efield-zt: - n = 0 - bQMMM = FALSE - QMconstraints = 0 - QMMMscheme = 0 - scalefactor = 1 -qm-opts: - ngQM = 0 -Using 1 MPI thread - -Detecting CPU-specific acceleration. -Present hardware specification: -Vendor: GenuineIntel -Brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Family: 6 Model: 58 Stepping: 9 -Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -Acceleration most likely to fit this hardware: AVX_256 -Acceleration selected at GROMACS compile time: AVX_256 - -Table routines are used for coulomb: FALSE -Table routines are used for vdw: TRUE -Will do PME sum in reciprocal space. - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen -A smooth particle mesh Ewald method -J. Chem. Phys. 103 (1995) pp. 8577-8592 --------- -------- --- Thank You --- -------- -------- - -Will do ordinary reciprocal space Ewald sum. -Using a Gaussian width (1/beta) of 0.433663 nm for Ewald -Using shifted Lennard-Jones, switch between 1.2 and 1.25 nm -Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.25 -Long Range LJ corr.: 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:51:39 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.74015e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.32056e+01 2.58625e+02 -2.66312e-11 5.76142e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.74015e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.32056e+01 2.58625e+02 -2.66312e-11 5.76142e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -7.61061e+01 2.02645e+01 -2.79015e+01 - 2.02646e+01 -1.87161e+01 -3.56389e+01 - -2.79014e+01 -3.56392e+01 1.06425e+02 - - Pressure (bar) - 1.03418e+02 -2.51450e+01 3.09020e+01 - -2.51451e+01 3.22750e+01 4.49428e+01 - 3.09019e+01 4.49432e+01 -1.18408e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.001 0.002 14.1 - Force 1 1 1 0.003 0.006 50.8 - PME mesh 1 1 1 0.001 0.002 16.2 - Write traj. 1 1 1 0.000 0.001 8.3 - Update 1 1 1 0.000 0.000 0.2 - Rest 1 0.001 0.001 10.4 ------------------------------------------------------------------------------ - Total 1 0.005 0.012 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 1.6 - PME 3D-FFT 1 1 2 0.000 0.001 7.3 - PME solve 1 1 1 0.000 0.001 7.0 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.005 45.0 - (ns/day) (hour/ns) -Performance: 32.317 0.743 -Finished mdrun on node 0 Fri Jun 20 15:51:39 2014 diff --git a/testing/inputs/Gromacs/UnitTest/angle1/mdout.mdp b/testing/inputs/Gromacs/UnitTest/angle1/mdout.mdp deleted file mode 100644 index e8ee4528..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle1/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/angle1/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/angle1/topol.tpr b/testing/inputs/Gromacs/UnitTest/angle1/topol.tpr deleted file mode 100644 index 016a4c10864245ab9a21d2f0325aa2d9a49f45e2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4312 zcmdT{eN0!<}hVaj#%M4o#nIYmlzt^66SJzOSiSZ;q&N;tx z&b{Z}``&#;QIvE=QPP^K8yaitHXBR@<^m%TB=Lks!a71SA*tKl?%v+xCR4eA5CbD9 zuw{Ub5n}(DU|d%#`AAZ|dTQuTxE~5!+qi}3I6|y*i=Kc!lRLZGd$txCOE~6ohQ~~W z9IJDM$4X2bbJhJVhB5WMsrIyO@91nt0`@JgdW$|#pce<|0Pk`XNp^9_uB(xF$#&N0 zISHtD)f6L%Z3NiHktGol8+Z12+)tB5HX)(T)8_8h-9T=)yT?N=dPbiHLf&k#(_YE@E|37IByZ{J51u_wz-pLWbuX1gw%Yma0FG8BdRa;3lCNT|p< z@RjLx?-0j1pZUs7%a_b~o}(OJNn7VCTU@&@D6DN6&6`~>`IV5~@W!<3v6xX?P+N}= zl)C1Bonq~n85wo%&g=~7vx?$;v+I2a>mOTNo$sD&b+86MZ8Yj}=vng5&{`z79YvOT-;Mvsg7rV$$w`KLtv*tS1S4h-diFa9_ zJ+X&1#rPi5)1u9>zqmZ870hO{rsCKjt{TU7CVoBUf~El8Z$KB!g(&{$(F)kbSHJ{pt5LX~bopr^%-^Oxm75l&tPg>=V_!ZR!(0 zAJ+1|+@Y;mDAc+azOh*zKj<^`zhFB!pW@Hz|3z(BcB-#sr}_%B2W-cN_xk?$Ax-=3 zl`nh~XTP)M?mQ_{76!EEoHKrB{&}tFkkhu5Gq0`RaavkDzVYFL{g!#yvDSx9P5s5k z{X|DXKpxw=PZVo1Nz`r44}X8@gWs!q>BStMNm2d85rTqq#WT+w=8jcIMn=^!uu7cj z)wTTpT?})GIL4^fOQ8P5J4T~rt!ENEo;T~_i9KZE&S%7zyjpsU{BV(^kMuiQ1HHJ7hzpfVuW8&Y_vDQXtA87em(->7_UK2QE&!9 zX<>tOi{*})6uTkB;5}i9w+H$Oj+gW`2mWQv{X*-o`{@$jt0;B@F{==qJKsB8CInlN HHJ|IBodE{1 diff --git a/testing/inputs/Gromacs/UnitTest/angle2/confout.gro b/testing/inputs/Gromacs/UnitTest/angle2/confout.gro deleted file mode 100644 index e42c8e99..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle2/confout.gro +++ /dev/null @@ -1,12 +0,0 @@ -Ethanol - 9 - 1ETH CB 1 2.711 2.946 2.803 0.1006 -0.3737 0.2468 - 1ETH HB1 2 2.709 2.847 2.757 1.3518 3.0856 0.8708 - 1ETH HB2 3 2.616 2.954 2.855 -0.6358 -0.5466 -0.9490 - 1ETH OG1 4 2.804 2.957 2.907 0.1840 -0.1568 0.3435 - 1ETH HG1 5 2.883 2.946 2.857 -2.3209 0.8242 1.1101 - 1ETH CG2 6 2.732 3.048 2.687 -0.1720 0.3703 -0.4977 - 1ETH HG21 7 2.833 3.064 2.649 -1.9416 -0.3611 0.1548 - 1ETH HG22 8 2.700 3.145 2.723 2.1709 -0.9620 -3.0497 - 1ETH HG23 9 2.663 3.035 2.603 -0.6942 0.4885 -0.5993 - 3.01061 3.01061 3.01061 diff --git a/testing/inputs/Gromacs/UnitTest/angle2/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/angle2/gromacs_stderr.txt deleted file mode 100644 index df1c36e3..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle2/gromacs_stderr.txt +++ /dev/null @@ -1,112 +0,0 @@ - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/angle2/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/angle2/angle2.gro Input Structure - file: gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/angle2/angle2.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/angle2/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/angle2/mdout.mdp to ./inputs/Gromacs/UnitTest/angle2/#mdout.mdp.26# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K - -WARNING 1 [file angle2.top, line 112]: - The bond in molecule-type Ethanol between atoms 4 OG1 and 5 HG1 has an - estimated oscillational period of 9.0e-03 ps, which is less than 5 times - the time step of 2.0e-03 ps. - Maybe you forgot to change the constraints mdp option. - -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -There was 1 warning - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/angle2/topol.tpr to ./inputs/Gromacs/UnitTest/angle2/#topol.tpr.26# - -gcq#42: "May the Force Be With You" (Star Wars) - diff --git a/testing/inputs/Gromacs/UnitTest/angle2/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/angle2/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle2/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/angle2/md.log b/testing/inputs/Gromacs/UnitTest/angle2/md.log deleted file mode 100644 index 4360d50d..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle2/md.log +++ /dev/null @@ -1,401 +0,0 @@ -Log file opened on Fri Jun 20 15:51:45 2014 -Host: Christophs-MacBook-Air.local pid: 23223 nodeid: 0 nnodes: 1 -Gromacs version: VERSION 4.6.3 -Precision: single -Memory model: 64 bit -MPI library: thread_mpi -OpenMP support: disabled -GPU support: disabled -invsqrt routine: gmx_software_invsqrt(x) -CPU acceleration: AVX_256 -FFT library: fftw-3.3.2-sse2 -Large file support: enabled -RDTSCP usage: enabled -Built on: Tue Nov 19 15:39:55 CST 2013 -Built by: CTK@vpn-user-1-38.itc.virginia.edu [CMAKE] -Build OS/arch: Darwin 13.0.0 x86_64 -Build CPU vendor: GenuineIntel -Build CPU brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Build CPU family: 6 Model: 58 Stepping: 9 -Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -C compiler: /usr/bin/gcc Clang Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1 -C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG - - - :-) G R O M A C S (-: - - GROup of MAchos and Cynical Suckers - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) mdrun (-: - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl -GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable -molecular simulation -J. Chem. Theory Comput. 4 (2008) pp. 435-447 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. -Berendsen -GROMACS: Fast, Flexible and Free -J. Comp. Chem. 26 (2005) pp. 1701-1719 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -E. Lindahl and B. Hess and D. van der Spoel -GROMACS 3.0: A package for molecular simulation and trajectory analysis -J. Mol. Mod. 7 (2001) pp. 306-317 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, D. van der Spoel and R. van Drunen -GROMACS: A message-passing parallel molecular dynamics implementation -Comp. Phys. Comm. 91 (1995) pp. 43-56 --------- -------- --- Thank You --- -------- -------- - -Input Parameters: - integrator = md-vv - nsteps = 0 - init-step = 0 - cutoff-scheme = Group - ns_type = Grid - nstlist = 10 - ndelta = 2 - nstcomm = 10 - comm-mode = Linear - nstlog = 1000 - nstxout = 1000 - nstvout = 1000 - nstfout = 0 - nstcalcenergy = 10 - nstenergy = 1000 - nstxtcout = 0 - init-t = 0 - delta-t = 0.002 - xtcprec = 1000 - fourierspacing = 0.12 - nkx = 28 - nky = 28 - nkz = 28 - pme-order = 4 - ewald-rtol = 1e-06 - ewald-geometry = 0 - epsilon-surface = 0 - optimize-fft = FALSE - ePBC = xyz - bPeriodicMols = FALSE - bContinuation = FALSE - bShakeSOR = FALSE - etc = Berendsen - bPrintNHChains = FALSE - nsttcouple = 1 - epc = Berendsen - epctype = Isotropic - nstpcouple = 1 - tau-p = 10 - ref-p (3x3): - ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} - ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} - ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} - compress (3x3): - compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} - compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} - compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} - refcoord-scaling = No - posres-com (3): - posres-com[0]= 0.00000e+00 - posres-com[1]= 0.00000e+00 - posres-com[2]= 0.00000e+00 - posres-comB (3): - posres-comB[0]= 0.00000e+00 - posres-comB[1]= 0.00000e+00 - posres-comB[2]= 0.00000e+00 - verlet-buffer-drift = 0.005 - rlist = 1.5 - rlistlong = 1.5 - nstcalclr = 0 - rtpi = 0.05 - coulombtype = PME - coulomb-modifier = None - rcoulomb-switch = 0 - rcoulomb = 1.5 - vdwtype = Switch - vdw-modifier = None - rvdw-switch = 1.2 - rvdw = 1.25 - epsilon-r = 1 - epsilon-rf = inf - tabext = 1 - implicit-solvent = No - gb-algorithm = Still - gb-epsilon-solvent = 80 - nstgbradii = 1 - rgbradii = 1 - gb-saltconc = 0 - gb-obc-alpha = 1 - gb-obc-beta = 0.8 - gb-obc-gamma = 4.85 - gb-dielectric-offset = 0.009 - sa-algorithm = Ace-approximation - sa-surface-tension = 2.05016 - DispCorr = AllEnerPres - bSimTemp = FALSE - free-energy = no - nwall = 0 - wall-type = 9-3 - wall-atomtype[0] = -1 - wall-atomtype[1] = -1 - wall-density[0] = 0 - wall-density[1] = 0 - wall-ewald-zfac = 3 - pull = no - rotation = FALSE - disre = No - disre-weighting = Conservative - disre-mixed = FALSE - dr-fc = 1000 - dr-tau = 0 - nstdisreout = 100 - orires-fc = 0 - orires-tau = 0 - nstorireout = 100 - dihre-fc = 0 - em-stepsize = 0.01 - em-tol = 10 - niter = 20 - fc-stepsize = 0 - nstcgsteep = 1000 - nbfgscorr = 10 - ConstAlg = Lincs - shake-tol = 0.0001 - lincs-order = 4 - lincs-warnangle = 30 - lincs-iter = 1 - bd-fric = 0 - ld-seed = 1993 - cos-accel = 0 - deform (3x3): - deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - adress = FALSE - userint1 = 0 - userint2 = 0 - userint3 = 0 - userint4 = 0 - userreal1 = 0 - userreal2 = 0 - userreal3 = 0 - userreal4 = 0 -grpopts: - nrdf: 24 - ref-t: 300 - tau-t: 10 -anneal: No -ann-npoints: 0 - acc: 0 0 0 - nfreeze: N N N - energygrp-flags[ 0]: 0 - efield-x: - n = 0 - efield-xt: - n = 0 - efield-y: - n = 0 - efield-yt: - n = 0 - efield-z: - n = 0 - efield-zt: - n = 0 - bQMMM = FALSE - QMconstraints = 0 - QMMMscheme = 0 - scalefactor = 1 -qm-opts: - ngQM = 0 -Using 1 MPI thread - -Detecting CPU-specific acceleration. -Present hardware specification: -Vendor: GenuineIntel -Brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Family: 6 Model: 58 Stepping: 9 -Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -Acceleration most likely to fit this hardware: AVX_256 -Acceleration selected at GROMACS compile time: AVX_256 - -Table routines are used for coulomb: FALSE -Table routines are used for vdw: TRUE -Will do PME sum in reciprocal space. - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen -A smooth particle mesh Ewald method -J. Chem. Phys. 103 (1995) pp. 8577-8592 --------- -------- --- Thank You --- -------- -------- - -Will do ordinary reciprocal space Ewald sum. -Using a Gaussian width (1/beta) of 0.433663 nm for Ewald -Using shifted Lennard-Jones, switch between 1.2 and 1.25 nm -Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.25 -Long Range LJ corr.: 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:51:45 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond G96Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 1.81487e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.54327e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.12368e+01 2.58625e+02 -2.66312e-11 5.76172e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond G96Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 1.81487e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.54327e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.12368e+01 2.58625e+02 -2.66312e-11 5.76172e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -7.14194e+01 1.74799e+01 -2.46667e+01 - 1.74800e+01 -1.48946e+01 -3.50673e+01 - -2.46663e+01 -3.50671e+01 9.79159e+01 - - Pressure (bar) - 9.77137e+01 -2.17560e+01 2.69651e+01 - -2.17561e+01 2.76240e+01 4.42471e+01 - 2.69646e+01 4.42468e+01 -1.08053e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 7.9 - Force 1 1 1 0.000 0.000 4.5 - PME mesh 1 1 1 0.001 0.003 50.9 - Write traj. 1 1 1 0.001 0.001 24.6 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 11.7 ------------------------------------------------------------------------------ - Total 1 0.002 0.005 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.2 - PME 3D-FFT 1 1 2 0.001 0.001 25.4 - PME solve 1 1 1 0.000 0.001 19.6 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 81.362 0.295 -Finished mdrun on node 0 Fri Jun 20 15:51:45 2014 diff --git a/testing/inputs/Gromacs/UnitTest/angle2/mdout.mdp b/testing/inputs/Gromacs/UnitTest/angle2/mdout.mdp deleted file mode 100644 index 307817d8..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle2/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/angle2/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/angle2/topol.tpr b/testing/inputs/Gromacs/UnitTest/angle2/topol.tpr deleted file mode 100644 index c2aa509339c4e21bd0ea9b141b76561c6b2a4cba..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4312 zcmdT{YfM~K5Wc*T0wP6evEl~btq@?B12Cyc^Nj_%g zo0)UwoOAEFi=rs0ilU@6RMyp3*Q_&H@~nAgB1mEh^@J6KL_$J`yT!e!(@myw3n2y8TRJxsn2R{((!yhw ze2&$)!ed1ij=5_77Q>jv-c)*;H?_94AOZUpQ@P$4D9}qe=m763FOclQkX=(H@sh1o z898yNcU2W4iERYf#*rlu;_J6|dfYFNMK&R>#?$QXFx)_Hhr825E_z0vCPL0lg37Ox zW#olpIdL+w$u}S#4AiQm%Hq;3)~@bP)<&NywS3+>RhH?xYOOw&5y(&!=1Y~HS~Fp7 z#=);GZ+rVW&iTxjt(m`K&G8)P_(Iw~Ro3L%eo0~NNNZf@dd;td^s09zTu(*qaRjyf zWN)!+`qy#RzP)c`Y1`A=LVEv&QSIIK4}Gi;&wZrrJ^!4KHTVg$*@#2$+cKt|&mLi| zUcNRU4(p$xZ$H`Ge@BdFL`&Q*m?<*Nx*i8@m#7K~n(lH(&_nLa)A(+DoiC z#(J^+@OoHN{Xbe4)g=+|J|+`V2)OTWC8QBK@YbR*vFjscCe3m z5l0?`?QBvf1N|E7|+R4`sC+4(mIwJ z=l2#Gd&>elR`)8(Qh@K3EDP20WTfRjaAxptM&r!!eZaklwcvhUl!)AI@xs11){Rp4uR+BXz>;85MT5TdYlfM3lUqZsc3fWeWODAhh&0vF7S` zqNrv{RIGSUJk(n(9zH!Ts;dr)yvluIb?a_XZhukSKhSSKlhxqU>qZ?fA4yaX#CMCz zu4eU_pO5M}Uv1Wx&E)GHGv7LFPapD`dR}oHnoja(^!%dM&1>q8%w%7FX0PMKz%Jh( zKc?uvz4@hY`GD-ClM+gee70*0#m^)e>9NeQ0 zfmLEuuc77t@1mGPqH zDKNI2EYA%deu>T3DCaEX%ek;iCXV7afr9r%zYOb!5+(eK;-I|=MhoRE^@~9W$9N5L zih?r;N)sETn{4+?COJ(Z2JZ<=tTWJ0aJ+ 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:51:51 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Bond-Cross Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 -9.77149e+02 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 -9.69865e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 -9.44061e+02 2.58625e+02 -2.66312e-11 1.49574e+02 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Bond-Cross Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 -9.77149e+02 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 -9.69865e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 -9.44061e+02 2.58625e+02 -2.66312e-11 1.49574e+02 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - 5.19994e+02 -1.67613e+02 8.67133e+01 - -1.67608e+02 -2.68972e+02 1.11004e+03 - 8.67124e+01 1.11003e+03 -5.93908e+02 - - Pressure (bar) - -6.22078e+02 2.03515e+02 -1.08592e+02 - 2.03509e+02 3.36854e+02 -1.34943e+03 - -1.08591e+02 -1.34942e+03 7.33946e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB VdW [V&F] 0.000013 0.000 0.0 - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.8 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.128 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 6.7 - Force 1 1 1 0.000 0.000 4.4 - PME mesh 1 1 1 0.001 0.002 51.4 - Write traj. 1 1 1 0.000 0.001 22.6 - Update 1 1 1 0.000 0.000 0.5 - Rest 1 0.000 0.001 14.5 ------------------------------------------------------------------------------ - Total 1 0.001 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.2 - PME 3D-FFT 1 1 2 0.000 0.001 23.0 - PME solve 1 1 1 0.000 0.001 22.3 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.001 0.001 100.0 - (ns/day) (hour/ns) -Performance: 119.011 0.202 -Finished mdrun on node 0 Fri Jun 20 15:51:51 2014 diff --git a/testing/inputs/Gromacs/UnitTest/angle3/mdout.mdp b/testing/inputs/Gromacs/UnitTest/angle3/mdout.mdp deleted file mode 100644 index 288186cd..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle3/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/angle3/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/angle3/topol.tpr b/testing/inputs/Gromacs/UnitTest/angle3/topol.tpr deleted file mode 100644 index 0cda2b7673f4c55191afa3b5ba37f2a0eaf4eb01..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4292 zcmdT{Z%kWN6o33j28ayphI2Ofe-i?oTb_MzjH=5fQ=ns;Mp3$e3P;!Hy@@piI zJTq1kCu2SN2E_f*T8&g)Mxos?F!)hz>Zuz0r#-WE7T*;|^U9V6Fc#PxAY4>bhr|*r63Tw5XW0UWdh!WT9-ahMlB4wW%)9w?) z)xNo3r{kLHxfWWkGx%6-oTu@*R=ad{Onjz)f*vDebFYbb{prF5vEX|~JG!OfL|XU) z=O^N|i4Ox}M|9i>*_@w{Uz~hQ99!IryvX8YPdq;XU-K@VML}qkHRrQ-hK5=y39O07 zeSzoDxJx{uG+!+mm}AX#tgn)2yE5-_KYwyJYl`umW2CJ#$Mf>ih+cNy!kUUxW4LA< z^<4T|%mqyWyvu+gmsAU`big_Uz7xP0fChh}pxQCDr4tEyY=!!#ZQLE`2ZCO1C9sdV@x5Rl^CONt2*=q++!EsvhmUnbcpVrI!fTOztVi~-CiG|A z)1(oXeU5|2c!~DFMKL^|ybkUK9QV##F>x3R!rbj-b1nC6=Fo$gLqFhn4!Kt5xK`#+ zyN-Y!AY5zaP;2HA?SnCp>CfHd-$B4U*k`seF54In-y%GR=mR$P1OA;c8?|hsmTj)Z z+BhFJ=fmcF*va%x>Hj<7^MuA;;*J0wCO}~04#0DRv)MqvZ64%HMC(X4&hITW_Lc>9x*k%LWPtCLEX&pMWTfRjaAxptMB~iy zeZYN)wcuV}k%-b=nZh;FAZ(qFi_)$2!cnD(^1hG7ecdC%o!>4TM_Pp~I3?WLps3A# zNH||DH1ZwiErNa%2ybDp*m&hzQRSZ%4Qt*J4-8j}2TxCn=B5Lptnq!Zp=YnCcRwfY z9UFC@DQ*wztyAiYhqAT(nS-Knpi6t|=fir*m)rGK^W}Qq{5PuW$%A3*&`avUxtvJR z&@Wo+l2?1vk{d3!46Db-_JsfVAy5D9wJ*X)e*8{dzw?yHnIG0)@XkcMr5E&yLtb^U zcurrt{fxADeB;f6{g!#ysqRNkPyfZI{X|DXKpxwMPZVo1NwlpUkA8pogWnql=*66z z$|y*CQ1HI!mtb92 zQba^iRN9+Zv{KH}J|Bm0jMpHiC^&j5j@Sd=wd!qfs#>@Je1OKw- fexVI`B6NxGQ527rm?Q+}&i4+N3Bguk&FA_jEk^zL diff --git a/testing/inputs/Gromacs/UnitTest/angle4/confout.gro b/testing/inputs/Gromacs/UnitTest/angle4/confout.gro deleted file mode 100644 index e42c8e99..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle4/confout.gro +++ /dev/null @@ -1,12 +0,0 @@ -Ethanol - 9 - 1ETH CB 1 2.711 2.946 2.803 0.1006 -0.3737 0.2468 - 1ETH HB1 2 2.709 2.847 2.757 1.3518 3.0856 0.8708 - 1ETH HB2 3 2.616 2.954 2.855 -0.6358 -0.5466 -0.9490 - 1ETH OG1 4 2.804 2.957 2.907 0.1840 -0.1568 0.3435 - 1ETH HG1 5 2.883 2.946 2.857 -2.3209 0.8242 1.1101 - 1ETH CG2 6 2.732 3.048 2.687 -0.1720 0.3703 -0.4977 - 1ETH HG21 7 2.833 3.064 2.649 -1.9416 -0.3611 0.1548 - 1ETH HG22 8 2.700 3.145 2.723 2.1709 -0.9620 -3.0497 - 1ETH HG23 9 2.663 3.035 2.603 -0.6942 0.4885 -0.5993 - 3.01061 3.01061 3.01061 diff --git a/testing/inputs/Gromacs/UnitTest/angle4/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/angle4/gromacs_stderr.txt deleted file mode 100644 index bba0e4d1..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle4/gromacs_stderr.txt +++ /dev/null @@ -1,112 +0,0 @@ - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/angle4/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/angle4/angle4.gro Input Structure - file: gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/angle4/angle4.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/angle4/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/angle4/mdout.mdp to ./inputs/Gromacs/UnitTest/angle4/#mdout.mdp.25# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K - -WARNING 1 [file angle4.top, line 112]: - The bond in molecule-type Ethanol between atoms 4 OG1 and 5 HG1 has an - estimated oscillational period of 9.0e-03 ps, which is less than 5 times - the time step of 2.0e-03 ps. - Maybe you forgot to change the constraints mdp option. - -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -There was 1 warning - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/angle4/topol.tpr to ./inputs/Gromacs/UnitTest/angle4/#topol.tpr.25# - -gcq#42: "May the Force Be With You" (Star Wars) - diff --git a/testing/inputs/Gromacs/UnitTest/angle4/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/angle4/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle4/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/angle4/md.log b/testing/inputs/Gromacs/UnitTest/angle4/md.log deleted file mode 100644 index af9a8c00..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle4/md.log +++ /dev/null @@ -1,401 +0,0 @@ -Log file opened on Fri Jun 20 15:51:57 2014 -Host: Christophs-MacBook-Air.local pid: 23248 nodeid: 0 nnodes: 1 -Gromacs version: VERSION 4.6.3 -Precision: single -Memory model: 64 bit -MPI library: thread_mpi -OpenMP support: disabled -GPU support: disabled -invsqrt routine: gmx_software_invsqrt(x) -CPU acceleration: AVX_256 -FFT library: fftw-3.3.2-sse2 -Large file support: enabled -RDTSCP usage: enabled -Built on: Tue Nov 19 15:39:55 CST 2013 -Built by: CTK@vpn-user-1-38.itc.virginia.edu [CMAKE] -Build OS/arch: Darwin 13.0.0 x86_64 -Build CPU vendor: GenuineIntel -Build CPU brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Build CPU family: 6 Model: 58 Stepping: 9 -Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -C compiler: /usr/bin/gcc Clang Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1 -C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG - - - :-) G R O M A C S (-: - - Good gRace! Old Maple Actually Chews Slate - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) mdrun (-: - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl -GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable -molecular simulation -J. Chem. Theory Comput. 4 (2008) pp. 435-447 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. -Berendsen -GROMACS: Fast, Flexible and Free -J. Comp. Chem. 26 (2005) pp. 1701-1719 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -E. Lindahl and B. Hess and D. van der Spoel -GROMACS 3.0: A package for molecular simulation and trajectory analysis -J. Mol. Mod. 7 (2001) pp. 306-317 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, D. van der Spoel and R. van Drunen -GROMACS: A message-passing parallel molecular dynamics implementation -Comp. Phys. Comm. 91 (1995) pp. 43-56 --------- -------- --- Thank You --- -------- -------- - -Input Parameters: - integrator = md-vv - nsteps = 0 - init-step = 0 - cutoff-scheme = Group - ns_type = Grid - nstlist = 10 - ndelta = 2 - nstcomm = 10 - comm-mode = Linear - nstlog = 1000 - nstxout = 1000 - nstvout = 1000 - nstfout = 0 - nstcalcenergy = 10 - nstenergy = 1000 - nstxtcout = 0 - init-t = 0 - delta-t = 0.002 - xtcprec = 1000 - fourierspacing = 0.12 - nkx = 28 - nky = 28 - nkz = 28 - pme-order = 4 - ewald-rtol = 1e-06 - ewald-geometry = 0 - epsilon-surface = 0 - optimize-fft = FALSE - ePBC = xyz - bPeriodicMols = FALSE - bContinuation = FALSE - bShakeSOR = FALSE - etc = Berendsen - bPrintNHChains = FALSE - nsttcouple = 1 - epc = Berendsen - epctype = Isotropic - nstpcouple = 1 - tau-p = 10 - ref-p (3x3): - ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} - ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} - ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} - compress (3x3): - compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} - compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} - compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} - refcoord-scaling = No - posres-com (3): - posres-com[0]= 0.00000e+00 - posres-com[1]= 0.00000e+00 - posres-com[2]= 0.00000e+00 - posres-comB (3): - posres-comB[0]= 0.00000e+00 - posres-comB[1]= 0.00000e+00 - posres-comB[2]= 0.00000e+00 - verlet-buffer-drift = 0.005 - rlist = 1.5 - rlistlong = 1.5 - nstcalclr = 0 - rtpi = 0.05 - coulombtype = PME - coulomb-modifier = None - rcoulomb-switch = 0 - rcoulomb = 1.5 - vdwtype = Switch - vdw-modifier = None - rvdw-switch = 1.2 - rvdw = 1.25 - epsilon-r = 1 - epsilon-rf = inf - tabext = 1 - implicit-solvent = No - gb-algorithm = Still - gb-epsilon-solvent = 80 - nstgbradii = 1 - rgbradii = 1 - gb-saltconc = 0 - gb-obc-alpha = 1 - gb-obc-beta = 0.8 - gb-obc-gamma = 4.85 - gb-dielectric-offset = 0.009 - sa-algorithm = Ace-approximation - sa-surface-tension = 2.05016 - DispCorr = AllEnerPres - bSimTemp = FALSE - free-energy = no - nwall = 0 - wall-type = 9-3 - wall-atomtype[0] = -1 - wall-atomtype[1] = -1 - wall-density[0] = 0 - wall-density[1] = 0 - wall-ewald-zfac = 3 - pull = no - rotation = FALSE - disre = No - disre-weighting = Conservative - disre-mixed = FALSE - dr-fc = 1000 - dr-tau = 0 - nstdisreout = 100 - orires-fc = 0 - orires-tau = 0 - nstorireout = 100 - dihre-fc = 0 - em-stepsize = 0.01 - em-tol = 10 - niter = 20 - fc-stepsize = 0 - nstcgsteep = 1000 - nbfgscorr = 10 - ConstAlg = Lincs - shake-tol = 0.0001 - lincs-order = 4 - lincs-warnangle = 30 - lincs-iter = 1 - bd-fric = 0 - ld-seed = 1993 - cos-accel = 0 - deform (3x3): - deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - adress = FALSE - userint1 = 0 - userint2 = 0 - userint3 = 0 - userint4 = 0 - userreal1 = 0 - userreal2 = 0 - userreal3 = 0 - userreal4 = 0 -grpopts: - nrdf: 24 - ref-t: 300 - tau-t: 10 -anneal: No -ann-npoints: 0 - acc: 0 0 0 - nfreeze: N N N - energygrp-flags[ 0]: 0 - efield-x: - n = 0 - efield-xt: - n = 0 - efield-y: - n = 0 - efield-yt: - n = 0 - efield-z: - n = 0 - efield-zt: - n = 0 - bQMMM = FALSE - QMconstraints = 0 - QMMMscheme = 0 - scalefactor = 1 -qm-opts: - ngQM = 0 -Using 1 MPI thread - -Detecting CPU-specific acceleration. -Present hardware specification: -Vendor: GenuineIntel -Brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Family: 6 Model: 58 Stepping: 9 -Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -Acceleration most likely to fit this hardware: AVX_256 -Acceleration selected at GROMACS compile time: AVX_256 - -Table routines are used for coulomb: FALSE -Table routines are used for vdw: TRUE -Will do PME sum in reciprocal space. - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen -A smooth particle mesh Ewald method -J. Chem. Phys. 103 (1995) pp. 8577-8592 --------- -------- --- Thank You --- -------- -------- - -Will do ordinary reciprocal space Ewald sum. -Using a Gaussian width (1/beta) of 0.433663 nm for Ewald -Using shifted Lennard-Jones, switch between 1.2 and 1.25 nm -Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.25 -Long Range LJ corr.: 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:51:57 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond BA-Cross Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 2.11547e+02 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.18831e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 2.44636e+02 2.58625e+02 -2.66312e-11 -7.62417e+03 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond BA-Cross Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 2.11547e+02 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.18831e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 2.44636e+02 2.58625e+02 -2.66312e-11 -7.62417e+03 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - 5.07895e+03 7.84720e+02 3.98258e+02 - 7.84726e+02 5.51886e+03 -2.48303e+03 - 3.98266e+02 -2.48302e+03 8.22107e+03 - - Pressure (bar) - -6.17065e+03 -9.55542e+02 -4.87764e+02 - -9.55548e+02 -6.70735e+03 3.02360e+03 - -4.87773e+02 3.02358e+03 -9.99451e+03 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB VdW [V&F] 0.000013 0.000 0.0 - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.8 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.128 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 6.4 - Force 1 1 1 0.000 0.000 4.1 - PME mesh 1 1 1 0.001 0.002 50.5 - Write traj. 1 1 1 0.000 0.001 23.8 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 14.7 ------------------------------------------------------------------------------ - Total 1 0.001 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.1 - PME 3D-FFT 1 1 2 0.000 0.001 22.7 - PME solve 1 1 1 0.000 0.001 22.0 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.001 0.001 99.8 - (ns/day) (hour/ns) -Performance: 115.816 0.207 -Finished mdrun on node 0 Fri Jun 20 15:51:57 2014 diff --git a/testing/inputs/Gromacs/UnitTest/angle4/mdout.mdp b/testing/inputs/Gromacs/UnitTest/angle4/mdout.mdp deleted file mode 100644 index e063d639..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle4/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/angle4/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/angle4/topol.tpr b/testing/inputs/Gromacs/UnitTest/angle4/topol.tpr deleted file mode 100644 index 8e2f62bf99c8e63355f74cd6239694b874558e1c..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4312 zcmdT{YfKzf6dvA40gs&U#td0IiAfBp>J8 z?>z3g_s-l|6h+Ba6eX*ruBo}fx5;WRaunH!AW0@P6V?#Y32EK_4*#|uKbgucgajC- zz?K0zL5KqvOuwO)8Y4&x8lllYvE!&?apMl6lL(2P%|-zFOz+y!(X*w*R>nTBC)Q^# zW}nX+>npRf&+Ge#4>gUwsSC7k>+I@40QN1ZZnIG+(n}5K2=A>ak?hi_?W>n~$@bJ6 zF)7IR)|VoPZ8+G*k);t*n|JmE{Lhm`HX+3qX!my;!$@qmzb8OL^o%~Ogo2v{r7sXX zPqA1{oQ(A}HXt61Hp!KkJ;Tws@~O8jj^fA{2%BN~OQiMySd= z__cjcaESdJ&wTa9`KykCz;X63rCn3iZQi#oE3DO=)=l2m!b()Hd*{6Osf7Kisa+=r z%DvOSO++>2BUddr_Y>Dat}#X(%8UBVIt%<1i&{oJ)zz+C9~PhMpQ7(D+1!6TUVk=s zR?K>z(~fN^Ihho?#PRWXZS*6**b%84CY$5q@^fQPh~snn5Eq^s>x{<7;Va*x^T`Pg zvF3Qz6~X?-QUYt@afjg9H0~F-D9l##dZ$@)9_#BQ+OE|5TrZy5&6<3C4;f+0jd8y^ zKd2X7w6Lb+L=y|@s27sgVlHTM;Qa;+!CdGyRMB{uHTzgEw;x^)Ys$Z&bx~dhVHF{h zkVU||c`G4@a2p|)fZDtk+$p$AWDY)g9505y3s#E9cLQ@kkjpmq74t$+7xP0<6L$nS z+)aoFhkJ}|^u;!wlN%A-=eSeQ69oO-PT(=-$9IIs=mCDjLD$M47TW`($RdC4CGIW)=D{Abjk;{39==a_4$%i} z><7kon>KRUMlRc&i?wk)Y>tP`@vv9YJB9!6gwGQidx<*&c$5HvjXMC(4bEl*0l#Oe z2_6E+VgIpTsKe)iJ;h$~9{$%c)Qa((tfWtV&f~3PrG9>Ip|Q6tu#@$mqO1h?Udggl zE>A{U?gM9r@y%$QIld3L3$Yg5$;%Q^xGPmS2Wy3`?MYF%wMIC~G*R6BiFlx6P`I*N zgyU$Fum#42OY0L=nU9Ey*K>_{$3=^v-vq*w+a)$$`%aYkrbO+Ucf~^k<>KKp6QZI1 zpeU;QKy2vTCu&?Ti2H|!TxauJLVDA<`tsp)?LcausOxRlp84g7Uhvg+ebr2{-aYfJ z>U{c8$lCvkdT2T$oY()W)->1w>n{#zw96X*k*X*g?Wa7?eB$vHeeuBoaB0qCc+ii{1mV@QF!DC$E47JKJOO54N z*cIoG;CFz6_eH+~Yf(uMVMS4CZ%l8g9Ho6R0%0GoK@L%H2Bx&JLAuR(&t!(%8fEaF tuq3-9{h0OAzG26|thrxk1MV 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:52:03 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond U-B Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 1.90482e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.63323e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.21364e+01 2.58625e+02 -2.66312e-11 -4.00070e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond U-B Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 1.90482e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.63323e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.21364e+01 2.58625e+02 -2.66312e-11 -4.00070e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -4.02939e+01 1.87616e+01 -1.62286e+01 - 1.87620e+01 -1.17369e-01 -3.99225e+01 - -1.62284e+01 -3.99228e+01 7.60768e+01 - - Pressure (bar) - 5.98317e+01 -2.33159e+01 1.66953e+01 - -2.33163e+01 9.63904e+00 5.01562e+01 - 1.66951e+01 5.01566e+01 -8.14728e+01 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB VdW [V&F] 0.000013 0.000 0.0 - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.8 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.128 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 6.4 - Force 1 1 1 0.000 0.000 4.5 - PME mesh 1 1 1 0.001 0.002 52.0 - Write traj. 1 1 1 0.000 0.001 21.7 - Update 1 1 1 0.000 0.000 0.5 - Rest 1 0.000 0.001 14.9 ------------------------------------------------------------------------------ - Total 1 0.002 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.6 - PME 3D-FFT 1 1 2 0.000 0.001 22.4 - PME solve 1 1 1 0.000 0.001 23.2 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 112.648 0.213 -Finished mdrun on node 0 Fri Jun 20 15:52:03 2014 diff --git a/testing/inputs/Gromacs/UnitTest/angle5/mdout.mdp b/testing/inputs/Gromacs/UnitTest/angle5/mdout.mdp deleted file mode 100644 index fd46a7d8..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle5/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/angle5/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/angle5/topol.tpr b/testing/inputs/Gromacs/UnitTest/angle5/topol.tpr deleted file mode 100644 index ab143e9e296832dcf3d117f774e54ded264ea51c..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4392 zcmdT{YfM~K5Wc*T0wP5zSnCGgtq@>gdG6k`yAT#1B|t->M%yAwNJT(cO-e+!8V!_S zeWeui2ND0MX{*tu*wVe*nrJnpiistpF@!&jHZ`;{q=txfzPmf?;kFx~H8D=|F*D!H zoHOT~d(T}IMM+i^C8?pZuD-fvv#B7*l4B-SIt#1jH&NUrKe?kTYD=Kuy0Y7Tl9efy*NMzc$XtjvhzcBO_jt;wzEpl zi9x-qDj!K~BfvI}ERGOczq8BZewHk<2{ARE7I&xa268*yT^@4LGx{_UvThJmzC>;& z&xp0e$=E=?4sm~=RwY#ylUiWu?)juN@?=TD=WR1(>8{I`>LY1^3`JqSMCq+H6H3z# zd{gkIcYx!Z&wSaY#Y>hf&ryyqr>!$(O|IP+6xOzs#?7u*{7Oi#e{0h9M8vQysIABQ zid?h5Pq21O4GlZ#*lii4cc->r<)2lQQ2gzV4;@DT=jP^6{QYyy4x=yUPnyk3>fujI zy&+PX>_eV^VYDrjABHb^m(DxIJHVRrSr>bIYx4=LiN~FUXI;Oq>>@kamexJX zn(J6!AyIe5-eZ0K#2(fZ<9kg{TWOB{<;8w2XF8oV6-NfKWE|U>=nTvSO#$2&fG(H| zz50r4FRy`Gy>tRjx*R?LHOCYQvBodMc_P4mjL($Ongek!|$FHlCB~6?`LbPoXaedb*Xs zK6=2niGB2eIPxGIXCLwOAdfhFtRKSb!FUi}lk8(%vX8Z)KmD6P8gbd@ICzX_+>3JJ z@O*Or+ygl7nYm2jFb0IV+sWoy?$^j+ZX<_2!0{Y%t;}()%%OHY0X;yt*2tmO$QjqK z4-n?h-NfHPz&zMrwlOZ-7!Th&JcsB5HueMlok1J5Y@?QKuEp9oA2#R1=6u+z>7CO5 zcf#ihjlIMj0X$5Az{VYb=LTo9k$~SvWdtXI^RWNeFO0+If<47v@*e)zIn;{&oUEo# ze$K3C(NF4VO4uXY2rho_|;TB-!h#p=r@6I zrnZYsm%kTbCbwK1)ejqls?Gp~`bK>5?0qg0^2A@_pZhP@i zyt+TOM^tvVs89WRSj+l)hqh)eSL>Yn&Q|{9L7%DjCELN-1bn(U+Uv zXFE2y*Z0>?N!lN;edQZF`-5%6&XXcxu1|ZxIpud|pV#sZIc*D>vs%WE)6(McjW-JR zTjpU$S|2$z@ed#M3mpjod2H)GQLM=%QMWZd`s1aK{;cSx7jtwfLG=?y2nx;>&pdOO zJ5n7Q8dgWZDp9Ie*Yf|15zHat7@=A(f%+5gna$;EJ>%f>(3(J|nvD^`c|s z8%2KRLblx$7+X%3=LQeIxZKw$=Pc*Txv+~T592q0g7-zc2A^h||2klKTnlERm zUk*Vy#%qvM6r4d&n%E%SRDRb~g54Bi@Sd 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:52:09 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Quartic Angles Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 1.16568e+02 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 1.23852e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 1.49656e+02 2.58625e+02 -2.66312e-11 5.76137e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Quartic Angles Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 1.16568e+02 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 1.23852e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 1.49656e+02 2.58625e+02 -2.66312e-11 5.76137e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -4.97232e+02 3.51638e+01 -1.79320e+02 - 3.51655e+01 -1.20075e+02 -6.55103e+01 - -1.79320e+02 -6.55103e+01 6.28910e+02 - - Pressure (bar) - 6.15958e+02 -4.32785e+01 2.15189e+02 - -4.32806e+01 1.55636e+02 8.12983e+01 - 2.15189e+02 8.12983e+01 -7.54310e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Quartic Angles 0.000013 0.002 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 6.5 - Force 1 1 1 0.000 0.000 5.3 - PME mesh 1 1 1 0.001 0.002 50.7 - Write traj. 1 1 1 0.000 0.001 22.6 - Update 1 1 1 0.000 0.000 0.5 - Rest 1 0.000 0.001 14.4 ------------------------------------------------------------------------------ - Total 1 0.002 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.3 - PME 3D-FFT 1 1 2 0.000 0.001 23.3 - PME solve 1 1 1 0.000 0.001 21.3 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 113.762 0.211 -Finished mdrun on node 0 Fri Jun 20 15:52:09 2014 diff --git a/testing/inputs/Gromacs/UnitTest/angle6/mdout.mdp b/testing/inputs/Gromacs/UnitTest/angle6/mdout.mdp deleted file mode 100644 index a51cd75d..00000000 --- a/testing/inputs/Gromacs/UnitTest/angle6/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/angle6/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/angle6/topol.tpr b/testing/inputs/Gromacs/UnitTest/angle6/topol.tpr deleted file mode 100644 index f976145e943d3bd8a4f2d7264c185f607563acc4..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4352 zcmdT{ZA_b06ux|nAscftlnrq<^LrBl6gr@^?`=!h;>QqJmZ;G&qzgd=glaP4w9{xn zvQ49bG5ta0mzr%FT{Z{n+s#DLjOk1qA&VjWQ!+CaLuQCL&-1pY-qlrxm>5s;^qljY zbM8I&-naK{g%B%*5b0apHMNyhn@vS|mOL{NB*}zY!fHY)VQIUs*|)vJN2a)ekN_hh zuvLIgkn-TUNZe5K`AE_NMr!mU){h3RZQMe15+TvG#YjM(sjY3z9oq`b#T@gxVq-=5 z9INui#)^wL=B@fm3}YI5rZ9O$Qkd`+VO1#CzFCx;cOw|@!G%#KG_x?H$*n)$K_`SAC*J1`;ix#9c+o_ z$KgxgrgK~w*u$FhS(gO5stXCMiN{@&N-*vrhs<4J&+MFJ&2_A=kZ8M8?y^01Y9DKg z@qJ~aU2l%#rMVtGZ#;`N6(>e;)j0NZ$!jndGzD-E0ES>L^cpOwzQCGetgp8pUJq-k z|3~Yhx-`Nv!g4}70q=zy3HUDGM93guY+eiQ9^5%9hnVWe%Q4Q4a!mxhUoZy*wQOTw zF)sw;Vtxq5#9aa|nSgw7xbN6TUu@$!S&ZQR#~p;;An5C60{iF#?;ZBh3*yLwaGZU_ zvm!j=@UaIFUK7TH@VZnVYg2u!5B(YUJ!!;MpX1;$p1L394goztxHgtUZ7ip*-6;N>k2@)L8v*lRZ`sDU zY-2pU$M77Y57^ib__s%F)Uu6Qwz(E-<9yhh51aF0FQj)$|KACpCp7jFcLeYt0RkI$ z0G=D1&3XcU_gD!o0_S1>v0oU6&jovmz2rUouXCss<2hMKpZuK1TgO7<{Jn+7-m<_> z)&ul=U;)7UN|pI)c{0*!A2>7ki_ti9ydQ7}VlB9fuS;a^?i5+xQz6X_kICFRr?eDn zGQa&Jc~5hXw5`}GEyrr4**`38+AdkP`~g|=N`{ed8PAgRn?SlUTIGhz-^k*s30blF zEqPz}MtT3~QCaCZB=g+w$@MM!rPKDTyt{9Y?M(L8pk6aQBC7HkYsR4}-_^W}7*+k4)V8jO60iHl83qR@7%MYCBBfvDIXC zZt(C+%7gW4&V0U_3%lg(QM~^JzAySTtZPbw3<+VUy@^B%)hz9^eh9~S4Qh(O8APOk z4blzecZ{VuOi>2k6P9HBcOi+4xAZFx{L7mAg*M;_(IwtX|AkD%EI@GXeD83Xlx)S< He6D{0uQvmM diff --git a/testing/inputs/Gromacs/UnitTest/bond1/confout.gro b/testing/inputs/Gromacs/UnitTest/bond1/confout.gro deleted file mode 100644 index e42c8e99..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond1/confout.gro +++ /dev/null @@ -1,12 +0,0 @@ -Ethanol - 9 - 1ETH CB 1 2.711 2.946 2.803 0.1006 -0.3737 0.2468 - 1ETH HB1 2 2.709 2.847 2.757 1.3518 3.0856 0.8708 - 1ETH HB2 3 2.616 2.954 2.855 -0.6358 -0.5466 -0.9490 - 1ETH OG1 4 2.804 2.957 2.907 0.1840 -0.1568 0.3435 - 1ETH HG1 5 2.883 2.946 2.857 -2.3209 0.8242 1.1101 - 1ETH CG2 6 2.732 3.048 2.687 -0.1720 0.3703 -0.4977 - 1ETH HG21 7 2.833 3.064 2.649 -1.9416 -0.3611 0.1548 - 1ETH HG22 8 2.700 3.145 2.723 2.1709 -0.9620 -3.0497 - 1ETH HG23 9 2.663 3.035 2.603 -0.6942 0.4885 -0.5993 - 3.01061 3.01061 3.01061 diff --git a/testing/inputs/Gromacs/UnitTest/bond1/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/bond1/gromacs_stderr.txt deleted file mode 100644 index d0bf3e8c..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond1/gromacs_stderr.txt +++ /dev/null @@ -1,112 +0,0 @@ - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/bond1/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/bond1/bond1.gro Input Structure file: - gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/bond1/bond1.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/bond1/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond1/mdout.mdp to ./inputs/Gromacs/UnitTest/bond1/#mdout.mdp.25# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K - -WARNING 1 [file bond1.top, line 112]: - The bond in molecule-type Ethanol between atoms 4 OG1 and 5 HG1 has an - estimated oscillational period of 9.0e-03 ps, which is less than 5 times - the time step of 2.0e-03 ps. - Maybe you forgot to change the constraints mdp option. - -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -There was 1 warning - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond1/topol.tpr to ./inputs/Gromacs/UnitTest/bond1/#topol.tpr.25# - -gcq#42: "May the Force Be With You" (Star Wars) - diff --git a/testing/inputs/Gromacs/UnitTest/bond1/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/bond1/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond1/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/bond1/md.log b/testing/inputs/Gromacs/UnitTest/bond1/md.log deleted file mode 100644 index 02ae480a..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond1/md.log +++ /dev/null @@ -1,401 +0,0 @@ -Log file opened on Fri Jun 20 15:52:15 2014 -Host: Christophs-MacBook-Air.local pid: 23288 nodeid: 0 nnodes: 1 -Gromacs version: VERSION 4.6.3 -Precision: single -Memory model: 64 bit -MPI library: thread_mpi -OpenMP support: disabled -GPU support: disabled -invsqrt routine: gmx_software_invsqrt(x) -CPU acceleration: AVX_256 -FFT library: fftw-3.3.2-sse2 -Large file support: enabled -RDTSCP usage: enabled -Built on: Tue Nov 19 15:39:55 CST 2013 -Built by: CTK@vpn-user-1-38.itc.virginia.edu [CMAKE] -Build OS/arch: Darwin 13.0.0 x86_64 -Build CPU vendor: GenuineIntel -Build CPU brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Build CPU family: 6 Model: 58 Stepping: 9 -Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -C compiler: /usr/bin/gcc Clang Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1 -C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG - - - :-) G R O M A C S (-: - - Guyana Rwanda Oman Macau Angola Cameroon Senegal - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) mdrun (-: - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl -GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable -molecular simulation -J. Chem. Theory Comput. 4 (2008) pp. 435-447 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. -Berendsen -GROMACS: Fast, Flexible and Free -J. Comp. Chem. 26 (2005) pp. 1701-1719 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -E. Lindahl and B. Hess and D. van der Spoel -GROMACS 3.0: A package for molecular simulation and trajectory analysis -J. Mol. Mod. 7 (2001) pp. 306-317 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, D. van der Spoel and R. van Drunen -GROMACS: A message-passing parallel molecular dynamics implementation -Comp. Phys. Comm. 91 (1995) pp. 43-56 --------- -------- --- Thank You --- -------- -------- - -Input Parameters: - integrator = md-vv - nsteps = 0 - init-step = 0 - cutoff-scheme = Group - ns_type = Grid - nstlist = 10 - ndelta = 2 - nstcomm = 10 - comm-mode = Linear - nstlog = 1000 - nstxout = 1000 - nstvout = 1000 - nstfout = 0 - nstcalcenergy = 10 - nstenergy = 1000 - nstxtcout = 0 - init-t = 0 - delta-t = 0.002 - xtcprec = 1000 - fourierspacing = 0.12 - nkx = 28 - nky = 28 - nkz = 28 - pme-order = 4 - ewald-rtol = 1e-06 - ewald-geometry = 0 - epsilon-surface = 0 - optimize-fft = FALSE - ePBC = xyz - bPeriodicMols = FALSE - bContinuation = FALSE - bShakeSOR = FALSE - etc = Berendsen - bPrintNHChains = FALSE - nsttcouple = 1 - epc = Berendsen - epctype = Isotropic - nstpcouple = 1 - tau-p = 10 - ref-p (3x3): - ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} - ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} - ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} - compress (3x3): - compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} - compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} - compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} - refcoord-scaling = No - posres-com (3): - posres-com[0]= 0.00000e+00 - posres-com[1]= 0.00000e+00 - posres-com[2]= 0.00000e+00 - posres-comB (3): - posres-comB[0]= 0.00000e+00 - posres-comB[1]= 0.00000e+00 - posres-comB[2]= 0.00000e+00 - verlet-buffer-drift = 0.005 - rlist = 1.5 - rlistlong = 1.5 - nstcalclr = 0 - rtpi = 0.05 - coulombtype = PME - coulomb-modifier = None - rcoulomb-switch = 0 - rcoulomb = 1.5 - vdwtype = Switch - vdw-modifier = None - rvdw-switch = 1.2 - rvdw = 1.25 - epsilon-r = 1 - epsilon-rf = inf - tabext = 1 - implicit-solvent = No - gb-algorithm = Still - gb-epsilon-solvent = 80 - nstgbradii = 1 - rgbradii = 1 - gb-saltconc = 0 - gb-obc-alpha = 1 - gb-obc-beta = 0.8 - gb-obc-gamma = 4.85 - gb-dielectric-offset = 0.009 - sa-algorithm = Ace-approximation - sa-surface-tension = 2.05016 - DispCorr = AllEnerPres - bSimTemp = FALSE - free-energy = no - nwall = 0 - wall-type = 9-3 - wall-atomtype[0] = -1 - wall-atomtype[1] = -1 - wall-density[0] = 0 - wall-density[1] = 0 - wall-ewald-zfac = 3 - pull = no - rotation = FALSE - disre = No - disre-weighting = Conservative - disre-mixed = FALSE - dr-fc = 1000 - dr-tau = 0 - nstdisreout = 100 - orires-fc = 0 - orires-tau = 0 - nstorireout = 100 - dihre-fc = 0 - em-stepsize = 0.01 - em-tol = 10 - niter = 20 - fc-stepsize = 0 - nstcgsteep = 1000 - nbfgscorr = 10 - ConstAlg = Lincs - shake-tol = 0.0001 - lincs-order = 4 - lincs-warnangle = 30 - lincs-iter = 1 - bd-fric = 0 - ld-seed = 1993 - cos-accel = 0 - deform (3x3): - deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - adress = FALSE - userint1 = 0 - userint2 = 0 - userint3 = 0 - userint4 = 0 - userreal1 = 0 - userreal2 = 0 - userreal3 = 0 - userreal4 = 0 -grpopts: - nrdf: 24 - ref-t: 300 - tau-t: 10 -anneal: No -ann-npoints: 0 - acc: 0 0 0 - nfreeze: N N N - energygrp-flags[ 0]: 0 - efield-x: - n = 0 - efield-xt: - n = 0 - efield-y: - n = 0 - efield-yt: - n = 0 - efield-z: - n = 0 - efield-zt: - n = 0 - bQMMM = FALSE - QMconstraints = 0 - QMMMscheme = 0 - scalefactor = 1 -qm-opts: - ngQM = 0 -Using 1 MPI thread - -Detecting CPU-specific acceleration. -Present hardware specification: -Vendor: GenuineIntel -Brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Family: 6 Model: 58 Stepping: 9 -Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -Acceleration most likely to fit this hardware: AVX_256 -Acceleration selected at GROMACS compile time: AVX_256 - -Table routines are used for coulomb: FALSE -Table routines are used for vdw: TRUE -Will do PME sum in reciprocal space. - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen -A smooth particle mesh Ewald method -J. Chem. Phys. 103 (1995) pp. 8577-8592 --------- -------- --- Thank You --- -------- -------- - -Will do ordinary reciprocal space Ewald sum. -Using a Gaussian width (1/beta) of 0.433663 nm for Ewald -Using shifted Lennard-Jones, switch between 1.2 and 1.25 nm -Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.25 -Long Range LJ corr.: 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:52:15 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.74015e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.32056e+01 2.58625e+02 -2.66312e-11 5.76142e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.74015e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.32056e+01 2.58625e+02 -2.66312e-11 5.76142e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -7.61061e+01 2.02645e+01 -2.79015e+01 - 2.02646e+01 -1.87161e+01 -3.56389e+01 - -2.79014e+01 -3.56392e+01 1.06425e+02 - - Pressure (bar) - 1.03418e+02 -2.51450e+01 3.09020e+01 - -2.51451e+01 3.22750e+01 4.49428e+01 - 3.09019e+01 4.49432e+01 -1.18408e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 7.1 - Force 1 1 1 0.000 0.000 6.4 - PME mesh 1 1 1 0.001 0.002 49.6 - Write traj. 1 1 1 0.000 0.001 21.3 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 15.1 ------------------------------------------------------------------------------ - Total 1 0.002 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.7 - PME 3D-FFT 1 1 2 0.000 0.001 22.5 - PME solve 1 1 1 0.000 0.001 20.5 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 108.613 0.221 -Finished mdrun on node 0 Fri Jun 20 15:52:15 2014 diff --git a/testing/inputs/Gromacs/UnitTest/bond1/mdout.mdp b/testing/inputs/Gromacs/UnitTest/bond1/mdout.mdp deleted file mode 100644 index d9f672f2..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond1/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/bond1/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/bond1/topol.tpr b/testing/inputs/Gromacs/UnitTest/bond1/topol.tpr deleted file mode 100644 index 016a4c10864245ab9a21d2f0325aa2d9a49f45e2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4312 zcmdT{eN0!<}hVaj#%M4o#nIYmlzt^66SJzOSiSZ;q&N;tx z&b{Z}``&#;QIvE=QPP^K8yaitHXBR@<^m%TB=Lks!a71SA*tKl?%v+xCR4eA5CbD9 zuw{Ub5n}(DU|d%#`AAZ|dTQuTxE~5!+qi}3I6|y*i=Kc!lRLZGd$txCOE~6ohQ~~W z9IJDM$4X2bbJhJVhB5WMsrIyO@91nt0`@JgdW$|#pce<|0Pk`XNp^9_uB(xF$#&N0 zISHtD)f6L%Z3NiHktGol8+Z12+)tB5HX)(T)8_8h-9T=)yT?N=dPbiHLf&k#(_YE@E|37IByZ{J51u_wz-pLWbuX1gw%Yma0FG8BdRa;3lCNT|p< z@RjLx?-0j1pZUs7%a_b~o}(OJNn7VCTU@&@D6DN6&6`~>`IV5~@W!<3v6xX?P+N}= zl)C1Bonq~n85wo%&g=~7vx?$;v+I2a>mOTNo$sD&b+86MZ8Yj}=vng5&{`z79YvOT-;Mvsg7rV$$w`KLtv*tS1S4h-diFa9_ zJ+X&1#rPi5)1u9>zqmZ870hO{rsCKjt{TU7CVoBUf~El8Z$KB!g(&{$(F)kbSHJ{pt5LX~bopr^%-^Oxm75l&tPg>=V_!ZR!(0 zAJ+1|+@Y;mDAc+azOh*zKj<^`zhFB!pW@Hz|3z(BcB-#sr}_%B2W-cN_xk?$Ax-=3 zl`nh~XTP)M?mQ_{76!EEoHKrB{&}tFkkhu5Gq0`RaavkDzVYFL{g!#yvDSx9P5s5k z{X|DXKpxw=PZVo1Nz`r44}X8@gWs!q>BStMNm2d85rTqq#WT+w=8jcIMn=^!uu7cj z)wTTpT?})GIL4^fOQ8P5J4T~rt!ENEo;T~_i9KZE&S%7zyjpsU{BV(^kMuiQ1HHJ7hzpfVuW8&Y_vDQXtA87em(->7_UK2QE&!9 zX<>tOi{*})6uTkB;5}i9w+H$Oj+gW`2mWQv{X*-o`{@$jt0;B@F{==qJKsB8CInlN HHJ|IBodE{1 diff --git a/testing/inputs/Gromacs/UnitTest/bond2/confout.gro b/testing/inputs/Gromacs/UnitTest/bond2/confout.gro deleted file mode 100644 index e42c8e99..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond2/confout.gro +++ /dev/null @@ -1,12 +0,0 @@ -Ethanol - 9 - 1ETH CB 1 2.711 2.946 2.803 0.1006 -0.3737 0.2468 - 1ETH HB1 2 2.709 2.847 2.757 1.3518 3.0856 0.8708 - 1ETH HB2 3 2.616 2.954 2.855 -0.6358 -0.5466 -0.9490 - 1ETH OG1 4 2.804 2.957 2.907 0.1840 -0.1568 0.3435 - 1ETH HG1 5 2.883 2.946 2.857 -2.3209 0.8242 1.1101 - 1ETH CG2 6 2.732 3.048 2.687 -0.1720 0.3703 -0.4977 - 1ETH HG21 7 2.833 3.064 2.649 -1.9416 -0.3611 0.1548 - 1ETH HG22 8 2.700 3.145 2.723 2.1709 -0.9620 -3.0497 - 1ETH HG23 9 2.663 3.035 2.603 -0.6942 0.4885 -0.5993 - 3.01061 3.01061 3.01061 diff --git a/testing/inputs/Gromacs/UnitTest/bond2/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/bond2/gromacs_stderr.txt deleted file mode 100644 index 5d745555..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond2/gromacs_stderr.txt +++ /dev/null @@ -1,112 +0,0 @@ - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/bond2/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/bond2/bond2.gro Input Structure file: - gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/bond2/bond2.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/bond2/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond2/mdout.mdp to ./inputs/Gromacs/UnitTest/bond2/#mdout.mdp.25# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K - -WARNING 1 [file bond2.top, line 112]: - The bond in molecule-type Ethanol between atoms 4 OG1 and 5 HG1 has an - estimated oscillational period of 6.7e-03 ps, which is less than 5 times - the time step of 2.0e-03 ps. - Maybe you forgot to change the constraints mdp option. - -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -There was 1 warning - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond2/topol.tpr to ./inputs/Gromacs/UnitTest/bond2/#topol.tpr.25# - -gcq#42: "May the Force Be With You" (Star Wars) - diff --git a/testing/inputs/Gromacs/UnitTest/bond2/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/bond2/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond2/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/bond2/md.log b/testing/inputs/Gromacs/UnitTest/bond2/md.log deleted file mode 100644 index f94a5068..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond2/md.log +++ /dev/null @@ -1,401 +0,0 @@ -Log file opened on Fri Jun 20 15:52:21 2014 -Host: Christophs-MacBook-Air.local pid: 23303 nodeid: 0 nnodes: 1 -Gromacs version: VERSION 4.6.3 -Precision: single -Memory model: 64 bit -MPI library: thread_mpi -OpenMP support: disabled -GPU support: disabled -invsqrt routine: gmx_software_invsqrt(x) -CPU acceleration: AVX_256 -FFT library: fftw-3.3.2-sse2 -Large file support: enabled -RDTSCP usage: enabled -Built on: Tue Nov 19 15:39:55 CST 2013 -Built by: CTK@vpn-user-1-38.itc.virginia.edu [CMAKE] -Build OS/arch: Darwin 13.0.0 x86_64 -Build CPU vendor: GenuineIntel -Build CPU brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Build CPU family: 6 Model: 58 Stepping: 9 -Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -C compiler: /usr/bin/gcc Clang Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1 -C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG - - - :-) G R O M A C S (-: - - Grunge ROck MAChoS - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) mdrun (-: - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl -GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable -molecular simulation -J. Chem. Theory Comput. 4 (2008) pp. 435-447 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. -Berendsen -GROMACS: Fast, Flexible and Free -J. Comp. Chem. 26 (2005) pp. 1701-1719 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -E. Lindahl and B. Hess and D. van der Spoel -GROMACS 3.0: A package for molecular simulation and trajectory analysis -J. Mol. Mod. 7 (2001) pp. 306-317 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, D. van der Spoel and R. van Drunen -GROMACS: A message-passing parallel molecular dynamics implementation -Comp. Phys. Comm. 91 (1995) pp. 43-56 --------- -------- --- Thank You --- -------- -------- - -Input Parameters: - integrator = md-vv - nsteps = 0 - init-step = 0 - cutoff-scheme = Group - ns_type = Grid - nstlist = 10 - ndelta = 2 - nstcomm = 10 - comm-mode = Linear - nstlog = 1000 - nstxout = 1000 - nstvout = 1000 - nstfout = 0 - nstcalcenergy = 10 - nstenergy = 1000 - nstxtcout = 0 - init-t = 0 - delta-t = 0.002 - xtcprec = 1000 - fourierspacing = 0.12 - nkx = 28 - nky = 28 - nkz = 28 - pme-order = 4 - ewald-rtol = 1e-06 - ewald-geometry = 0 - epsilon-surface = 0 - optimize-fft = FALSE - ePBC = xyz - bPeriodicMols = FALSE - bContinuation = FALSE - bShakeSOR = FALSE - etc = Berendsen - bPrintNHChains = FALSE - nsttcouple = 1 - epc = Berendsen - epctype = Isotropic - nstpcouple = 1 - tau-p = 10 - ref-p (3x3): - ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} - ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} - ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} - compress (3x3): - compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} - compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} - compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} - refcoord-scaling = No - posres-com (3): - posres-com[0]= 0.00000e+00 - posres-com[1]= 0.00000e+00 - posres-com[2]= 0.00000e+00 - posres-comB (3): - posres-comB[0]= 0.00000e+00 - posres-comB[1]= 0.00000e+00 - posres-comB[2]= 0.00000e+00 - verlet-buffer-drift = 0.005 - rlist = 1.5 - rlistlong = 1.5 - nstcalclr = 0 - rtpi = 0.05 - coulombtype = PME - coulomb-modifier = None - rcoulomb-switch = 0 - rcoulomb = 1.5 - vdwtype = Switch - vdw-modifier = None - rvdw-switch = 1.2 - rvdw = 1.25 - epsilon-r = 1 - epsilon-rf = inf - tabext = 1 - implicit-solvent = No - gb-algorithm = Still - gb-epsilon-solvent = 80 - nstgbradii = 1 - rgbradii = 1 - gb-saltconc = 0 - gb-obc-alpha = 1 - gb-obc-beta = 0.8 - gb-obc-gamma = 4.85 - gb-dielectric-offset = 0.009 - sa-algorithm = Ace-approximation - sa-surface-tension = 2.05016 - DispCorr = AllEnerPres - bSimTemp = FALSE - free-energy = no - nwall = 0 - wall-type = 9-3 - wall-atomtype[0] = -1 - wall-atomtype[1] = -1 - wall-density[0] = 0 - wall-density[1] = 0 - wall-ewald-zfac = 3 - pull = no - rotation = FALSE - disre = No - disre-weighting = Conservative - disre-mixed = FALSE - dr-fc = 1000 - dr-tau = 0 - nstdisreout = 100 - orires-fc = 0 - orires-tau = 0 - nstorireout = 100 - dihre-fc = 0 - em-stepsize = 0.01 - em-tol = 10 - niter = 20 - fc-stepsize = 0 - nstcgsteep = 1000 - nbfgscorr = 10 - ConstAlg = Lincs - shake-tol = 0.0001 - lincs-order = 4 - lincs-warnangle = 30 - lincs-iter = 1 - bd-fric = 0 - ld-seed = 1993 - cos-accel = 0 - deform (3x3): - deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - adress = FALSE - userint1 = 0 - userint2 = 0 - userint3 = 0 - userint4 = 0 - userreal1 = 0 - userreal2 = 0 - userreal3 = 0 - userreal4 = 0 -grpopts: - nrdf: 24 - ref-t: 300 - tau-t: 10 -anneal: No -ann-npoints: 0 - acc: 0 0 0 - nfreeze: N N N - energygrp-flags[ 0]: 0 - efield-x: - n = 0 - efield-xt: - n = 0 - efield-y: - n = 0 - efield-yt: - n = 0 - efield-z: - n = 0 - efield-zt: - n = 0 - bQMMM = FALSE - QMconstraints = 0 - QMMMscheme = 0 - scalefactor = 1 -qm-opts: - ngQM = 0 -Using 1 MPI thread - -Detecting CPU-specific acceleration. -Present hardware specification: -Vendor: GenuineIntel -Brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Family: 6 Model: 58 Stepping: 9 -Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -Acceleration most likely to fit this hardware: AVX_256 -Acceleration selected at GROMACS compile time: AVX_256 - -Table routines are used for coulomb: FALSE -Table routines are used for vdw: TRUE -Will do PME sum in reciprocal space. - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen -A smooth particle mesh Ewald method -J. Chem. Phys. 103 (1995) pp. 8577-8592 --------- -------- --- Thank You --- -------- -------- - -Will do ordinary reciprocal space Ewald sum. -Using a Gaussian width (1/beta) of 0.433663 nm for Ewald -Using shifted Lennard-Jones, switch between 1.2 and 1.25 nm -Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.25 -Long Range LJ corr.: 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:52:21 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - G96Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 5.72066e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 3.18116e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.76157e+01 2.58625e+02 -2.66312e-11 -4.64062e+01 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - G96Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 5.72066e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 3.18116e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.76157e+01 2.58625e+02 -2.66312e-11 -4.64062e+01 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -1.04240e+02 4.09276e+01 -6.41902e+01 - 4.09273e+01 5.77951e+01 -1.38651e+02 - -6.41906e+01 -1.38650e+02 1.86637e+02 - - Pressure (bar) - 1.37658e+02 -5.02935e+01 7.50680e+01 - -5.02930e+01 -6.08446e+01 1.70315e+02 - 7.50685e+01 1.70315e+02 -2.16032e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 5.9 - Force 1 1 1 0.000 0.000 4.1 - PME mesh 1 1 1 0.001 0.003 50.6 - Write traj. 1 1 1 0.001 0.001 25.1 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 13.9 ------------------------------------------------------------------------------ - Total 1 0.002 0.006 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.0 - PME 3D-FFT 1 1 2 0.001 0.001 24.8 - PME solve 1 1 1 0.000 0.001 20.1 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 70.848 0.339 -Finished mdrun on node 0 Fri Jun 20 15:52:21 2014 diff --git a/testing/inputs/Gromacs/UnitTest/bond2/mdout.mdp b/testing/inputs/Gromacs/UnitTest/bond2/mdout.mdp deleted file mode 100644 index 878471b3..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond2/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/bond2/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/bond2/topol.tpr b/testing/inputs/Gromacs/UnitTest/bond2/topol.tpr deleted file mode 100644 index f24857454d9c1080a0e6e118dad183be7396193e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4312 zcmdT{ZA_b06n^CPSxPR00w< zqh^fh4>J6rF55J^3^&%d&P1nS)0sFzmSy43qKk&@2bm$_JkQ&ndaX2oGclgz={e^) z=iYnn$9vzmilU?|ijvk`)!0;1|A?tL-;!@8f+U{ML|8*eCM0!x+C5u(JY*_25n^D3 z1hx#&F+vt;>K-6#}Q&(8}$U#ncUgc-m|IDT*5K8D>7DG zz_EIFWUQo^WA6ID#n7j|HdWrXEghZhNWi+qRc+Ke3fAHT9pv54Ldh-)+x68FFWIhY zJtqO}-PJ`%VjBUrv1Lhw#HQ^%Ue7aRkxfXb_qKVubvKyX?dkE7i<(iViI97PkoO&S z$|6`zoQxdub%+PZB2fty35H@z?~ViIv8T$4Kk2wwVRT=!)Evvy6X=KeGNr%4OeoJh z^i}a2z9EitKJyjp7Oq-yy~jDel(stG@2j282!!?i3oq18)+tuj+N+th2eQ^%SsNbB zuPf;5u!gjAYGj}5bwg)ZpH~#un_cfYSzl;vb-jD3)yW$CS+iM>Lr;@`DQBFudgc1C z_*DBCbqC1i`lIpMQ-(P)=YCo}wyE&*IR9nNkH)K`A9_Sru-^dLoFA2+AA3w3pWlnT z!2DQ8I6n$s_BQQLhHr>9=d&*L^*0m|SQC%)gR`mMFAkBHZqMwUVa@GWUnfy_Cf;j% z?&NOP6yx)#r!6Hktc}`pxIGzV{ z*~Fn=2y?fS&24!OksRuYG)&u@sAscPkMq9SIE#}7gusI(#=fhq}?Ueq%6W&i~tR?OU zpq2oEjprZd279xXfbW?Kf{Va;SbwY+`r&=Snqn<^4gc#LDn&mhE2)#ud9-<~G|ta0 zG}e{{cD&|Ol$8MQD_NFm%Y%`Y>%gADzY&c+$GZV{Bj$oTdRZd!b|wnzV5Km(JTCG! zJB6i06$RZNiTm3Jg)O~VSjHQL**hU@>JCw!`j9An#h~X~rj3HW353hgDb`*4R+Q9V z6qRe<5)Te+5bGyTi<;^~BEM?CSlh8zIBn00`-X>XXR@39TH}QM#Ush;!NeV+s<%yj z@~5L(?w8xNRkHl26lrv8`ghi6g(nf<@0jSDVymoe2}U>vZY7~bRm{f9K| z*Vn%AkDvd}p0oXwNSPhbo_9?JTzQwZ!XqyGeD;i%we5^FdA#Ez1?w&Iuw!j?lc)dW z<9?(qAs~-!-6x7QnI!7wtq*^H^@HCkd+EU(n@Ujw#1TS*eZ`q)4r9lvBP09NQLsv! z>eIFS|1O3(M4Y44)<>ZF#5-oQb+vZ_JkFbK?&NMVapyDQOZqmPAU{&%GZ(fUreNQ4 zvOG3;_@!3=Ryk)WU(SVHdiE&33luyr+7(!fN{k37ik;Rb6fKgo)XzpB9OF62DGK%= zBrR-^Zn54ymEtgk89XN}@s40Uq5hJ-=D@$Kxn5`;jsRWadlbcCB4!1Gedl|Jn+d^I Ibj|zv2kM*y_W%F@ diff --git a/testing/inputs/Gromacs/UnitTest/bond3/confout.gro b/testing/inputs/Gromacs/UnitTest/bond3/confout.gro deleted file mode 100644 index e42c8e99..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond3/confout.gro +++ /dev/null @@ -1,12 +0,0 @@ -Ethanol - 9 - 1ETH CB 1 2.711 2.946 2.803 0.1006 -0.3737 0.2468 - 1ETH HB1 2 2.709 2.847 2.757 1.3518 3.0856 0.8708 - 1ETH HB2 3 2.616 2.954 2.855 -0.6358 -0.5466 -0.9490 - 1ETH OG1 4 2.804 2.957 2.907 0.1840 -0.1568 0.3435 - 1ETH HG1 5 2.883 2.946 2.857 -2.3209 0.8242 1.1101 - 1ETH CG2 6 2.732 3.048 2.687 -0.1720 0.3703 -0.4977 - 1ETH HG21 7 2.833 3.064 2.649 -1.9416 -0.3611 0.1548 - 1ETH HG22 8 2.700 3.145 2.723 2.1709 -0.9620 -3.0497 - 1ETH HG23 9 2.663 3.035 2.603 -0.6942 0.4885 -0.5993 - 3.01061 3.01061 3.01061 diff --git a/testing/inputs/Gromacs/UnitTest/bond3/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/bond3/gromacs_stderr.txt deleted file mode 100644 index e520aaf5..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond3/gromacs_stderr.txt +++ /dev/null @@ -1,103 +0,0 @@ - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/bond3/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/bond3/bond3.gro Input Structure file: - gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/bond3/bond3.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/bond3/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond3/mdout.mdp to ./inputs/Gromacs/UnitTest/bond3/#mdout.mdp.25# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond3/topol.tpr to ./inputs/Gromacs/UnitTest/bond3/#topol.tpr.25# - -gcq#42: "May the Force Be With You" (Star Wars) - diff --git a/testing/inputs/Gromacs/UnitTest/bond3/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/bond3/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond3/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/bond3/md.log b/testing/inputs/Gromacs/UnitTest/bond3/md.log deleted file mode 100644 index b396ab62..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond3/md.log +++ /dev/null @@ -1,401 +0,0 @@ -Log file opened on Fri Jun 20 15:52:27 2014 -Host: Christophs-MacBook-Air.local pid: 23314 nodeid: 0 nnodes: 1 -Gromacs version: VERSION 4.6.3 -Precision: single -Memory model: 64 bit -MPI library: thread_mpi -OpenMP support: disabled -GPU support: disabled -invsqrt routine: gmx_software_invsqrt(x) -CPU acceleration: AVX_256 -FFT library: fftw-3.3.2-sse2 -Large file support: enabled -RDTSCP usage: enabled -Built on: Tue Nov 19 15:39:55 CST 2013 -Built by: CTK@vpn-user-1-38.itc.virginia.edu [CMAKE] -Build OS/arch: Darwin 13.0.0 x86_64 -Build CPU vendor: GenuineIntel -Build CPU brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Build CPU family: 6 Model: 58 Stepping: 9 -Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -C compiler: /usr/bin/gcc Clang Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1 -C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG - - - :-) G R O M A C S (-: - - S C A M O R G - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) mdrun (-: - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl -GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable -molecular simulation -J. Chem. Theory Comput. 4 (2008) pp. 435-447 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. -Berendsen -GROMACS: Fast, Flexible and Free -J. Comp. Chem. 26 (2005) pp. 1701-1719 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -E. Lindahl and B. Hess and D. van der Spoel -GROMACS 3.0: A package for molecular simulation and trajectory analysis -J. Mol. Mod. 7 (2001) pp. 306-317 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, D. van der Spoel and R. van Drunen -GROMACS: A message-passing parallel molecular dynamics implementation -Comp. Phys. Comm. 91 (1995) pp. 43-56 --------- -------- --- Thank You --- -------- -------- - -Input Parameters: - integrator = md-vv - nsteps = 0 - init-step = 0 - cutoff-scheme = Group - ns_type = Grid - nstlist = 10 - ndelta = 2 - nstcomm = 10 - comm-mode = Linear - nstlog = 1000 - nstxout = 1000 - nstvout = 1000 - nstfout = 0 - nstcalcenergy = 10 - nstenergy = 1000 - nstxtcout = 0 - init-t = 0 - delta-t = 0.002 - xtcprec = 1000 - fourierspacing = 0.12 - nkx = 28 - nky = 28 - nkz = 28 - pme-order = 4 - ewald-rtol = 1e-06 - ewald-geometry = 0 - epsilon-surface = 0 - optimize-fft = FALSE - ePBC = xyz - bPeriodicMols = FALSE - bContinuation = FALSE - bShakeSOR = FALSE - etc = Berendsen - bPrintNHChains = FALSE - nsttcouple = 1 - epc = Berendsen - epctype = Isotropic - nstpcouple = 1 - tau-p = 10 - ref-p (3x3): - ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} - ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} - ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} - compress (3x3): - compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} - compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} - compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} - refcoord-scaling = No - posres-com (3): - posres-com[0]= 0.00000e+00 - posres-com[1]= 0.00000e+00 - posres-com[2]= 0.00000e+00 - posres-comB (3): - posres-comB[0]= 0.00000e+00 - posres-comB[1]= 0.00000e+00 - posres-comB[2]= 0.00000e+00 - verlet-buffer-drift = 0.005 - rlist = 1.5 - rlistlong = 1.5 - nstcalclr = 0 - rtpi = 0.05 - coulombtype = PME - coulomb-modifier = None - rcoulomb-switch = 0 - rcoulomb = 1.5 - vdwtype = Switch - vdw-modifier = None - rvdw-switch = 1.2 - rvdw = 1.25 - epsilon-r = 1 - epsilon-rf = inf - tabext = 1 - implicit-solvent = No - gb-algorithm = Still - gb-epsilon-solvent = 80 - nstgbradii = 1 - rgbradii = 1 - gb-saltconc = 0 - gb-obc-alpha = 1 - gb-obc-beta = 0.8 - gb-obc-gamma = 4.85 - gb-dielectric-offset = 0.009 - sa-algorithm = Ace-approximation - sa-surface-tension = 2.05016 - DispCorr = AllEnerPres - bSimTemp = FALSE - free-energy = no - nwall = 0 - wall-type = 9-3 - wall-atomtype[0] = -1 - wall-atomtype[1] = -1 - wall-density[0] = 0 - wall-density[1] = 0 - wall-ewald-zfac = 3 - pull = no - rotation = FALSE - disre = No - disre-weighting = Conservative - disre-mixed = FALSE - dr-fc = 1000 - dr-tau = 0 - nstdisreout = 100 - orires-fc = 0 - orires-tau = 0 - nstorireout = 100 - dihre-fc = 0 - em-stepsize = 0.01 - em-tol = 10 - niter = 20 - fc-stepsize = 0 - nstcgsteep = 1000 - nbfgscorr = 10 - ConstAlg = Lincs - shake-tol = 0.0001 - lincs-order = 4 - lincs-warnangle = 30 - lincs-iter = 1 - bd-fric = 0 - ld-seed = 1993 - cos-accel = 0 - deform (3x3): - deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - adress = FALSE - userint1 = 0 - userint2 = 0 - userint3 = 0 - userint4 = 0 - userreal1 = 0 - userreal2 = 0 - userreal3 = 0 - userreal4 = 0 -grpopts: - nrdf: 24 - ref-t: 300 - tau-t: 10 -anneal: No -ann-npoints: 0 - acc: 0 0 0 - nfreeze: N N N - energygrp-flags[ 0]: 0 - efield-x: - n = 0 - efield-xt: - n = 0 - efield-y: - n = 0 - efield-yt: - n = 0 - efield-z: - n = 0 - efield-zt: - n = 0 - bQMMM = FALSE - QMconstraints = 0 - QMMMscheme = 0 - scalefactor = 1 -qm-opts: - ngQM = 0 -Using 1 MPI thread - -Detecting CPU-specific acceleration. -Present hardware specification: -Vendor: GenuineIntel -Brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Family: 6 Model: 58 Stepping: 9 -Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -Acceleration most likely to fit this hardware: AVX_256 -Acceleration selected at GROMACS compile time: AVX_256 - -Table routines are used for coulomb: FALSE -Table routines are used for vdw: TRUE -Will do PME sum in reciprocal space. - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen -A smooth particle mesh Ewald method -J. Chem. Phys. 103 (1995) pp. 8577-8592 --------- -------- --- Thank You --- -------- -------- - -Will do ordinary reciprocal space Ewald sum. -Using a Gaussian width (1/beta) of 0.433663 nm for Ewald -Using shifted Lennard-Jones, switch between 1.2 and 1.25 nm -Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.25 -Long Range LJ corr.: 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:52:27 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Morse Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 7.95057e+01 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 1.05597e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 1.31401e+02 2.58625e+02 -2.66312e-11 2.25835e+03 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Morse Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 7.95057e+01 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 1.05597e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 1.31401e+02 2.58625e+02 -2.66312e-11 2.25835e+03 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -3.85408e+03 2.52426e+02 -9.76510e+02 - 2.52424e+02 4.61032e+02 -1.20592e+03 - -9.76495e+02 -1.20589e+03 -2.14783e+03 - - Pressure (bar) - 4.70148e+03 -3.07702e+02 1.18543e+03 - -3.07700e+02 -5.51612e+02 1.46925e+03 - 1.18541e+03 1.46922e+03 2.62518e+03 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Angles 0.000013 0.002 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Morse Potent. 0.000008 0.001 0.0 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.131 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 6.4 - Force 1 1 1 0.000 0.000 4.6 - PME mesh 1 1 1 0.001 0.002 49.9 - Write traj. 1 1 1 0.000 0.001 24.1 - Update 1 1 1 0.000 0.000 0.5 - Rest 1 0.000 0.001 14.6 ------------------------------------------------------------------------------ - Total 1 0.001 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.2 - PME 3D-FFT 1 1 2 0.000 0.001 21.8 - PME solve 1 1 1 0.000 0.001 22.1 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.001 0.001 99.9 - (ns/day) (hour/ns) -Performance: 117.792 0.204 -Finished mdrun on node 0 Fri Jun 20 15:52:27 2014 diff --git a/testing/inputs/Gromacs/UnitTest/bond3/mdout.mdp b/testing/inputs/Gromacs/UnitTest/bond3/mdout.mdp deleted file mode 100644 index 5596db5a..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond3/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/bond3/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/bond3/topol.tpr b/testing/inputs/Gromacs/UnitTest/bond3/topol.tpr deleted file mode 100644 index e82ed69ff68ab2f5eb0274fe372446e510fbc37a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4344 zcmdT{YfM~46u!KX0^$~>#flqzw?cr0<+*!j_d-~FbOSUbnrK^O38@GOt4WFIHbw&y ztgk?+{vhHXHElK86kED?TN6doRxz=JG=}h}(MCi2gVYeQp6~9Sb-H#1tcmd?ALpCz zoS8W@bMM?mQIvE=QPP@f8XD`|Tg}D!)_e;IWbuSX!UjSzA*tKb?%CPnA*$R!hye*1 zxD3cKLL4|7iW_dFHj-4IksAIJ*$xM;O>QAMju5MDGZIi|a%We2&-Ow~3CCPoWURP= zV{TVutfZJ@F85zz7}MCB8gJXqj?Q)@VBg|uwiyEjYjHvj>Mm!Y#EZh*T`TDl*J_QN z1oU^+79oi_0?ct_Nrc44-928LM>WaLoWfVh_!nM$ZkFcn*S`#!9QohmQ>q+_l!%XQgWcQn&Tpg*jaEB*BrLPh4m zFNXZ2U&d1y2FI|A1kb3$^;o>VIa>G4`vi zhu6cN`v0SKQ9rz^>j;Jov6~8*?F! zJQ&Bhjd)f_M;vXe5ymxRJQ&w4w^6&?M*XPIxX;NWF1I-j9pkOEUP@7_2zWkuOmpR76_Y2P->Hx=npnZFYqc3yxWzK!EHqHmv0oU6&jovmz2rUouXCsr<2hMNo&20fTgO`C z{NBQ2Z`r`(b)TZF1^8acwo+f7jJ#Y2&J6AA@i=pQ7jQRXEx4msWg>4+qNp0I7M7Mr zMcxjlu$HKzp!*|nPy3*-r8f!dM1!z+CxuPz6BVfsh_V+=M!t16OVDoup_w|xmdoFW z68D^_-teZlZ=h7%f9kZTt34?4Yu*)`JN5~u?P+oM$dK(!c9UOkn6y84I9WZA*e7aw z+tkN@I-=)(u}fdKP@s1&d~L6K?2zBw|GfRsd`cj*{};7kSyNxlO7$0H4cL#54Eulo zK287irO*8n=f1V)?4A-S3j_MI+Dt&pyPy{y*6d5!^ZLeJXQajB8y{)dZ&?SAwLNs| z^q+d%k8~siG>2!^{8w#ju8mbBy}>2vnbV+hVC&@12B>=gqcwaxYQb`Hc9ImrIXRJJRH5F3cU~ z;Mj7qJU4W-%c}g%a?VO^ITyTa`Urj(D0pA=i(uEZ7!jcVCuna%(IPoZ{cIG*FxDPq2+$=ytSAmMDQhsCJKsCp LO$cVuJ)i3zH6{cl diff --git a/testing/inputs/Gromacs/UnitTest/bond4/confout.gro b/testing/inputs/Gromacs/UnitTest/bond4/confout.gro deleted file mode 100644 index e42c8e99..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond4/confout.gro +++ /dev/null @@ -1,12 +0,0 @@ -Ethanol - 9 - 1ETH CB 1 2.711 2.946 2.803 0.1006 -0.3737 0.2468 - 1ETH HB1 2 2.709 2.847 2.757 1.3518 3.0856 0.8708 - 1ETH HB2 3 2.616 2.954 2.855 -0.6358 -0.5466 -0.9490 - 1ETH OG1 4 2.804 2.957 2.907 0.1840 -0.1568 0.3435 - 1ETH HG1 5 2.883 2.946 2.857 -2.3209 0.8242 1.1101 - 1ETH CG2 6 2.732 3.048 2.687 -0.1720 0.3703 -0.4977 - 1ETH HG21 7 2.833 3.064 2.649 -1.9416 -0.3611 0.1548 - 1ETH HG22 8 2.700 3.145 2.723 2.1709 -0.9620 -3.0497 - 1ETH HG23 9 2.663 3.035 2.603 -0.6942 0.4885 -0.5993 - 3.01061 3.01061 3.01061 diff --git a/testing/inputs/Gromacs/UnitTest/bond4/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/bond4/gromacs_stderr.txt deleted file mode 100644 index 2d5062f0..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond4/gromacs_stderr.txt +++ /dev/null @@ -1,103 +0,0 @@ - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/bond4/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/bond4/bond4.gro Input Structure file: - gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/bond4/bond4.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/bond4/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond4/mdout.mdp to ./inputs/Gromacs/UnitTest/bond4/#mdout.mdp.25# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond4/topol.tpr to ./inputs/Gromacs/UnitTest/bond4/#topol.tpr.25# - -gcq#42: "May the Force Be With You" (Star Wars) - diff --git a/testing/inputs/Gromacs/UnitTest/bond4/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/bond4/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond4/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/bond4/md.log b/testing/inputs/Gromacs/UnitTest/bond4/md.log deleted file mode 100644 index 7d3b0144..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond4/md.log +++ /dev/null @@ -1,401 +0,0 @@ -Log file opened on Fri Jun 20 15:52:33 2014 -Host: Christophs-MacBook-Air.local pid: 23325 nodeid: 0 nnodes: 1 -Gromacs version: VERSION 4.6.3 -Precision: single -Memory model: 64 bit -MPI library: thread_mpi -OpenMP support: disabled -GPU support: disabled -invsqrt routine: gmx_software_invsqrt(x) -CPU acceleration: AVX_256 -FFT library: fftw-3.3.2-sse2 -Large file support: enabled -RDTSCP usage: enabled -Built on: Tue Nov 19 15:39:55 CST 2013 -Built by: CTK@vpn-user-1-38.itc.virginia.edu [CMAKE] -Build OS/arch: Darwin 13.0.0 x86_64 -Build CPU vendor: GenuineIntel -Build CPU brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Build CPU family: 6 Model: 58 Stepping: 9 -Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -C compiler: /usr/bin/gcc Clang Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1 -C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG - - - :-) G R O M A C S (-: - - Great Red Oystrich Makes All Chemists Sane - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) mdrun (-: - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl -GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable -molecular simulation -J. Chem. Theory Comput. 4 (2008) pp. 435-447 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. -Berendsen -GROMACS: Fast, Flexible and Free -J. Comp. Chem. 26 (2005) pp. 1701-1719 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -E. Lindahl and B. Hess and D. van der Spoel -GROMACS 3.0: A package for molecular simulation and trajectory analysis -J. Mol. Mod. 7 (2001) pp. 306-317 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, D. van der Spoel and R. van Drunen -GROMACS: A message-passing parallel molecular dynamics implementation -Comp. Phys. Comm. 91 (1995) pp. 43-56 --------- -------- --- Thank You --- -------- -------- - -Input Parameters: - integrator = md-vv - nsteps = 0 - init-step = 0 - cutoff-scheme = Group - ns_type = Grid - nstlist = 10 - ndelta = 2 - nstcomm = 10 - comm-mode = Linear - nstlog = 1000 - nstxout = 1000 - nstvout = 1000 - nstfout = 0 - nstcalcenergy = 10 - nstenergy = 1000 - nstxtcout = 0 - init-t = 0 - delta-t = 0.002 - xtcprec = 1000 - fourierspacing = 0.12 - nkx = 28 - nky = 28 - nkz = 28 - pme-order = 4 - ewald-rtol = 1e-06 - ewald-geometry = 0 - epsilon-surface = 0 - optimize-fft = FALSE - ePBC = xyz - bPeriodicMols = FALSE - bContinuation = FALSE - bShakeSOR = FALSE - etc = Berendsen - bPrintNHChains = FALSE - nsttcouple = 1 - epc = Berendsen - epctype = Isotropic - nstpcouple = 1 - tau-p = 10 - ref-p (3x3): - ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} - ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} - ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} - compress (3x3): - compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} - compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} - compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} - refcoord-scaling = No - posres-com (3): - posres-com[0]= 0.00000e+00 - posres-com[1]= 0.00000e+00 - posres-com[2]= 0.00000e+00 - posres-comB (3): - posres-comB[0]= 0.00000e+00 - posres-comB[1]= 0.00000e+00 - posres-comB[2]= 0.00000e+00 - verlet-buffer-drift = 0.005 - rlist = 1.5 - rlistlong = 1.5 - nstcalclr = 0 - rtpi = 0.05 - coulombtype = PME - coulomb-modifier = None - rcoulomb-switch = 0 - rcoulomb = 1.5 - vdwtype = Switch - vdw-modifier = None - rvdw-switch = 1.2 - rvdw = 1.25 - epsilon-r = 1 - epsilon-rf = inf - tabext = 1 - implicit-solvent = No - gb-algorithm = Still - gb-epsilon-solvent = 80 - nstgbradii = 1 - rgbradii = 1 - gb-saltconc = 0 - gb-obc-alpha = 1 - gb-obc-beta = 0.8 - gb-obc-gamma = 4.85 - gb-dielectric-offset = 0.009 - sa-algorithm = Ace-approximation - sa-surface-tension = 2.05016 - DispCorr = AllEnerPres - bSimTemp = FALSE - free-energy = no - nwall = 0 - wall-type = 9-3 - wall-atomtype[0] = -1 - wall-atomtype[1] = -1 - wall-density[0] = 0 - wall-density[1] = 0 - wall-ewald-zfac = 3 - pull = no - rotation = FALSE - disre = No - disre-weighting = Conservative - disre-mixed = FALSE - dr-fc = 1000 - dr-tau = 0 - nstdisreout = 100 - orires-fc = 0 - orires-tau = 0 - nstorireout = 100 - dihre-fc = 0 - em-stepsize = 0.01 - em-tol = 10 - niter = 20 - fc-stepsize = 0 - nstcgsteep = 1000 - nbfgscorr = 10 - ConstAlg = Lincs - shake-tol = 0.0001 - lincs-order = 4 - lincs-warnangle = 30 - lincs-iter = 1 - bd-fric = 0 - ld-seed = 1993 - cos-accel = 0 - deform (3x3): - deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - adress = FALSE - userint1 = 0 - userint2 = 0 - userint3 = 0 - userint4 = 0 - userreal1 = 0 - userreal2 = 0 - userreal3 = 0 - userreal4 = 0 -grpopts: - nrdf: 24 - ref-t: 300 - tau-t: 10 -anneal: No -ann-npoints: 0 - acc: 0 0 0 - nfreeze: N N N - energygrp-flags[ 0]: 0 - efield-x: - n = 0 - efield-xt: - n = 0 - efield-y: - n = 0 - efield-yt: - n = 0 - efield-z: - n = 0 - efield-zt: - n = 0 - bQMMM = FALSE - QMconstraints = 0 - QMMMscheme = 0 - scalefactor = 1 -qm-opts: - ngQM = 0 -Using 1 MPI thread - -Detecting CPU-specific acceleration. -Present hardware specification: -Vendor: GenuineIntel -Brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Family: 6 Model: 58 Stepping: 9 -Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -Acceleration most likely to fit this hardware: AVX_256 -Acceleration selected at GROMACS compile time: AVX_256 - -Table routines are used for coulomb: FALSE -Table routines are used for vdw: TRUE -Will do PME sum in reciprocal space. - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen -A smooth particle mesh Ewald method -J. Chem. Phys. 103 (1995) pp. 8577-8592 --------- -------- --- Thank You --- -------- -------- - -Will do ordinary reciprocal space Ewald sum. -Using a Gaussian width (1/beta) of 0.433663 nm for Ewald -Using shifted Lennard-Jones, switch between 1.2 and 1.25 nm -Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.25 -Long Range LJ corr.: 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:52:33 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Cubic Bonds Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.03909e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.71300e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.29341e+01 2.58625e+02 -2.66312e-11 -4.13718e+01 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Cubic Bonds Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.03909e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.71300e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.29341e+01 2.58625e+02 -2.66312e-11 -4.13718e+01 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -4.19476e+01 1.93273e+01 -2.24763e+01 - 1.93274e+01 1.15659e+01 -4.81967e+01 - -2.24758e+01 -4.81968e+01 1.58165e+02 - - Pressure (bar) - 6.18444e+01 -2.40043e+01 2.42993e+01 - -2.40045e+01 -4.58034e+00 6.02265e+01 - 2.42986e+01 6.02267e+01 -1.81379e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Angles 0.000013 0.002 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Cubic Bonds 0.000008 0.000 0.0 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 5.9 - Force 1 1 1 0.000 0.000 4.1 - PME mesh 1 1 1 0.001 0.002 52.0 - Write traj. 1 1 1 0.000 0.001 24.2 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 13.4 ------------------------------------------------------------------------------ - Total 1 0.002 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.3 - PME 3D-FFT 1 1 2 0.000 0.001 24.4 - PME solve 1 1 1 0.000 0.001 21.4 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 103.112 0.233 -Finished mdrun on node 0 Fri Jun 20 15:52:33 2014 diff --git a/testing/inputs/Gromacs/UnitTest/bond4/mdout.mdp b/testing/inputs/Gromacs/UnitTest/bond4/mdout.mdp deleted file mode 100644 index c767893e..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond4/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/bond4/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/bond4/topol.tpr b/testing/inputs/Gromacs/UnitTest/bond4/topol.tpr deleted file mode 100644 index ac4286cdd21db58e6032a7265fecf3f2e44935a2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4296 zcmdT{YfM~K5Wc*T0wP6evEl~btq@>gdG6k`dm$`7N`Qt$jkZOWkcxn?nv{rcH5w?v z`U({E2ND0MX{*tu*wVe*nkbr5#l#ZQ7{Z@Mn;O~}QbWW#-`$<{xON4siE)ze&dfJ+ z&YAPL=k6+slB_67QbT23eRa)NQ$da;$4mrCG@+ibfe=rK>vXlcc6PbQRIVdLzz7Iz z8K5JCIB+HqH`Gc#l2nh88hnKM!NApxn~07gL~7fN1k@Sd-qG5%JSimu7&0k{Z(^#8IcgxPU_Escd-J&YD86Ej+ae(&oPDh?(=LhYYDv6hDt;)!W zL3?LaK9bl*fNgA993i%TcbD7sBw1t=Vrtwiu1>@C=XScf+~lHW)M+AQT_Z3@842Wv zVm)y(GRZd}?k0;wC6vXa7FfD_J}8ZxEGhW7ZLTccdD&8ZG|fn$2lFLLZ>^b7ns)Gu zf>%8Q9Or!I%eE|EvShiBaeO6hohxh71{KA*_kvtauDZ9aiD@whW^7LEJFF0zwtY2EXzxgF~(B!=#3Z)ngV>zgE^?xTU>jAwGogW ztF4FU!td|B|# zz<3b!!#36!H9#;1YJs4C+z;SzFCiZs?l87dBilGL;RN?J?hK3z!I(D^*vA<7POy)0 z5Jw(_|#`LH=3Hs`}$OYM~YzZ2e1 zXsjjf2;hDK1UBA#oEz-TW&(b{lo2!n=VAS^Ug(GS1#616MwE?&wvC$lenx%KIyX zx#?k%y~80ag{sKy{7~H0+Aplh4Z<>BC(P~%VO4uXY2tmN_{CHs-!hvn=r@7TQrpFr z%U_GanmJLi;SF(5Uy-=?)Rd^MIw*1~-w~VJ_6vvgDRJk}fc11ngIBMcuswS?UOf=o zBPzRF)W?22qGx@+OJBE;t9LGZWh;O5kk{1vobAwjf-kN2C$(-_Q(s9>^ya4b*^Unl zdVl*aN&n@g&%EPjzp-WRo)ifSefl%nj8Drxujd`sY)cvQ`o>+SrOD$PA1YXHnTH)| zec;s8AAHmgv?T=Ov2FN7u_lv5-O>2qx0l}gwW6C|%(0mS)khp5AlO%&dFC*7q&hr2 zqK<-9qEwHe<^OXL%pu|!rM4ad)hFIEo6Fa`C&1&pSr#7nVe2QYDwFyM?8>E}cZ<|T5n}Q796P9SZzn(yUabI%aU)EeNv;n)1F7ZJ{v73llgJ9qJ O-r;6KuoYhOzWxr)bNsjf diff --git a/testing/inputs/Gromacs/UnitTest/bond5/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/bond5/gromacs_stderr.txt deleted file mode 100644 index cda2e81a..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond5/gromacs_stderr.txt +++ /dev/null @@ -1,118 +0,0 @@ - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/bond5/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/bond5/bond5.gro Input Structure file: - gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/bond5/bond5.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/bond5/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond5/mdout.mdp to ./inputs/Gromacs/UnitTest/bond5/#mdout.mdp.23# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - - -ERROR 1 [file bond5.top, line 14]: - Not enough parameters - - -ERROR 2 [file bond5.top, line 15]: - Not enough parameters - - -ERROR 3 [file bond5.top, line 16]: - Not enough parameters - - -ERROR 4 [file bond5.top, line 17]: - Not enough parameters - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K - -There were 3 notes - -------------------------------------------------------- -Program grompp, VERSION 4.6.3 -Source code file: /Users/CTK/Builds/gromacs-4.6.3/source/src/kernel/grompp.c, line: 1593 - -Fatal error: -There were 4 errors in input file(s) -For more information and tips for troubleshooting, please check the GROMACS -website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------- - -"May the Force Be With You" (Star Wars) - diff --git a/testing/inputs/Gromacs/UnitTest/bond5/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/bond5/gromacs_stdout.txt deleted file mode 100644 index e69de29b..00000000 diff --git a/testing/inputs/Gromacs/UnitTest/bond5/mdout.mdp b/testing/inputs/Gromacs/UnitTest/bond5/mdout.mdp deleted file mode 100644 index 286c8cc7..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond5/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/bond5/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/bond6/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/bond6/gromacs_stderr.txt deleted file mode 100644 index 86d06c90..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond6/gromacs_stderr.txt +++ /dev/null @@ -1,112 +0,0 @@ - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/bond6/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/bond6/bond6.gro Input Structure file: - gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/bond6/bond6.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/bond6/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond6/mdout.mdp to ./inputs/Gromacs/UnitTest/bond6/#mdout.mdp.24# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K - -WARNING 1 [file bond6.top, line 112]: - The bond in molecule-type Ethanol between atoms 4 OG1 and 5 HG1 has an - estimated oscillational period of 9.0e-03 ps, which is less than 5 times - the time step of 2.0e-03 ps. - Maybe you forgot to change the constraints mdp option. - -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -There was 1 warning - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond6/topol.tpr to ./inputs/Gromacs/UnitTest/bond6/#topol.tpr.24# - -gcq#42: "May the Force Be With You" (Star Wars) - diff --git a/testing/inputs/Gromacs/UnitTest/bond6/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/bond6/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond6/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/bond6/mdout.mdp b/testing/inputs/Gromacs/UnitTest/bond6/mdout.mdp deleted file mode 100644 index ca87afb1..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond6/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/bond6/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:44 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/bond6/topol.tpr b/testing/inputs/Gromacs/UnitTest/bond6/topol.tpr deleted file mode 100644 index 63e5a0fee9b119c8415809bf7c9bae48e089b33e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4048 zcmdT{ZA_b06n^WBjl4mA@B%ZW^bOUKJX;PP`&9kH1Lr}SiGzK6f zz_Nml5#r#vP+T`F`AAZIdTRJ5(hmog2e%O&M;hzgswbe&G{Nm{^>pcOFt^Lo?IjmIqfZlQ&J8MhkTr$; zNL^2ytl8x2D()vlqLNl57>X=Cy&spyo-Ql;tbMk^=(=jDJ(j5_&=2!vN?)Csv^?|B z*G2n$gB<64<|{TYU9seNk8^w_Yn`oVcI~;Ou(f40ZE?L4P{MZ8n^UeQVn%EsYdzUt z;+p$ylC5KUc*MEK&=I!h6~*~h=LZh9Kee1@wh|qZ0h%mUF4?QGJEFOavj@iBtRdv|7u-Shj(!uX)0+NDen85Ni#@qAvKUHkq2=^-c=vVg9Gy2o-YqE&TKF7ghyyezN^mS569-dEL6ZZv< z*TGyCaTpiE-0g(9me&x;p`S<&y@BI7fL0~q@O|IQFbEo0O&=31Y#I@p@tQP6(^oE6P(J z7NxHm^nA;VQP8(gI1L?Q^VRP}v3pijZFpNe&|e}RIx{J1YYvIL>i5Ni?FWRz`kc6T zXwZ5#tI@C3PuN~OlB^y~>=o5Lt?E<19My8Z+NrIZ&)2%e#<;?to4yIlYjGZKhu$rB9F1|6UCMwiMqY%(I2jS_(xR_{e3z% zouUSaBMk}870)hnm^)S-9v)Fg!76d8Pq*^_H8IQ~;uxh`A1U=G-Zh&m*Lx?x<9V|# zoZ3qecO7ed@#`fg$d45HnG0jPDLA&AEYA%derct@NzPfxmvezjr;g%#sNj9kE(0wq zF(RNSHrks|6#u`3Mg3wJ!ZBV$I1Yd_2uU*ovdxuuO{dsRVFvFBOT0bUPiVZPZ#eKD hTkaQDS9^f|mfx=^b`vpc5S%;TJ6t9Nqv)2;^)KXx1Tg>r diff --git a/testing/inputs/Gromacs/UnitTest/bond7/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/bond7/gromacs_stderr.txt deleted file mode 100644 index d4f96f0e..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond7/gromacs_stderr.txt +++ /dev/null @@ -1,103 +0,0 @@ - :-) G R O M A C S (-: - - Gnomes, ROck Monsters And Chili Sauce - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/bond7/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/bond7/bond7.gro Input Structure file: - gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/bond7/bond7.top Input Topology file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/bond7/topol.tpr Output Run input file: - tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond7/mdout.mdp to ./inputs/Gromacs/UnitTest/bond7/#mdout.mdp.23# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/bond7/topol.tpr to ./inputs/Gromacs/UnitTest/bond7/#topol.tpr.23# - -gcq#155: "Shake Yourself" (YES) - diff --git a/testing/inputs/Gromacs/UnitTest/bond7/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/bond7/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond7/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/bond7/mdout.mdp b/testing/inputs/Gromacs/UnitTest/bond7/mdout.mdp deleted file mode 100644 index 9e6de8ae..00000000 --- a/testing/inputs/Gromacs/UnitTest/bond7/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/bond7/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:45 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/bond7/topol.tpr b/testing/inputs/Gromacs/UnitTest/bond7/topol.tpr deleted file mode 100644 index 107cfe67e5ab65a86e73bb70d9bc4a5042bc915d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4280 zcmdT{YfM~K5Wc*T0wP6evEl~btq@>gdF}2!yBEUZqZ^#P*KXuB`>;Vvf1A@K{kk z$K0;)SaA`@T<)u4nA13$DsRj7w)R#e;M`)WwipvF)#3!b#JijYl3f_G-PIB=*;=)c z6NmAx>Ov&3jR4!YvIIhW{mw40=V`LYCd9eDEuK!pUCQnBba}}|&8X8v$hl5n9T`dF zhhr^qGP21xAnqlLL?u+jr59Pcdp;_UK3P`uY1>Rirt7k$=17K-K!2DoQ+jL7gz}67 zUlqOX8{jzSGheZ3@scISdz9nLY1>RilWX?{#h%u<+4WLDv2S=|()C!>uFUVk!uUd+3mQjcscI3D9a&-syfb>u^j=vbOJKsM(` zz?Z#E=bz>qV9oigOMShyg#^~bqetM`Gx~=^|<`kkq6;8`-o=- zdBovkPY|vV^Fg>y*+;Fik9tv`(T_pOz#%>^>1_+N0=P)*$TgjOilhU6%3AYij4$hoy z%*!_B!}kZz8|r|K^MHSQ(8gG{F_vu}i@k9^Y|e+x`LI`0JEi~cgzpm?XNevGJV=1R z#=DN^26wZOfZr<>1dYIXIDecM=HYw6nc^(@4FBsKD#dtCR#PWG=aKfY+BmrZWZoCJ`cMlHOPG>dv^}2EU^M?}E{qa4bs=Gyf;^)J9 z&X+s%HFNoT=iE1T>*ELgrrsCq2WOK48NI)#b&Hz%T4u68KeNw%Y;dptj~`O>-(LB` zKX&#zd-l$gB5AHqe@>eUXu0S0ffBVd&n)n{n= z|F<; Fe*zv&`4|8I diff --git a/testing/inputs/Gromacs/UnitTest/dihedral1/confout.gro b/testing/inputs/Gromacs/UnitTest/dihedral1/confout.gro deleted file mode 100644 index e42c8e99..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral1/confout.gro +++ /dev/null @@ -1,12 +0,0 @@ -Ethanol - 9 - 1ETH CB 1 2.711 2.946 2.803 0.1006 -0.3737 0.2468 - 1ETH HB1 2 2.709 2.847 2.757 1.3518 3.0856 0.8708 - 1ETH HB2 3 2.616 2.954 2.855 -0.6358 -0.5466 -0.9490 - 1ETH OG1 4 2.804 2.957 2.907 0.1840 -0.1568 0.3435 - 1ETH HG1 5 2.883 2.946 2.857 -2.3209 0.8242 1.1101 - 1ETH CG2 6 2.732 3.048 2.687 -0.1720 0.3703 -0.4977 - 1ETH HG21 7 2.833 3.064 2.649 -1.9416 -0.3611 0.1548 - 1ETH HG22 8 2.700 3.145 2.723 2.1709 -0.9620 -3.0497 - 1ETH HG23 9 2.663 3.035 2.603 -0.6942 0.4885 -0.5993 - 3.01061 3.01061 3.01061 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral1/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/dihedral1/gromacs_stderr.txt deleted file mode 100644 index aa2af720..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral1/gromacs_stderr.txt +++ /dev/null @@ -1,113 +0,0 @@ - :-) G R O M A C S (-: - - Gnomes, ROck Monsters And Chili Sauce - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/dihedral1/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/dihedral1/dihedral1.gro Input - Structure file: gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/dihedral1/dihedral1.top Input Topology - file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/dihedral1/topol.tpr Output Run input - file: tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/dihedral1/mdout.mdp to ./inputs/Gromacs/UnitTest/dihedral1/#mdout.mdp.25# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K - -WARNING 1 [file dihedral1.top, line 112]: - The bond in molecule-type Ethanol between atoms 4 OG1 and 5 HG1 has an - estimated oscillational period of 9.0e-03 ps, which is less than 5 times - the time step of 2.0e-03 ps. - Maybe you forgot to change the constraints mdp option. - -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -There was 1 warning - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/dihedral1/topol.tpr to ./inputs/Gromacs/UnitTest/dihedral1/#topol.tpr.25# - -gcq#155: "Shake Yourself" (YES) - diff --git a/testing/inputs/Gromacs/UnitTest/dihedral1/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/dihedral1/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral1/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/dihedral1/md.log b/testing/inputs/Gromacs/UnitTest/dihedral1/md.log deleted file mode 100644 index 5c84b6ef..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral1/md.log +++ /dev/null @@ -1,401 +0,0 @@ -Log file opened on Fri Jun 20 15:52:45 2014 -Host: Christophs-MacBook-Air.local pid: 23348 nodeid: 0 nnodes: 1 -Gromacs version: VERSION 4.6.3 -Precision: single -Memory model: 64 bit -MPI library: thread_mpi -OpenMP support: disabled -GPU support: disabled -invsqrt routine: gmx_software_invsqrt(x) -CPU acceleration: AVX_256 -FFT library: fftw-3.3.2-sse2 -Large file support: enabled -RDTSCP usage: enabled -Built on: Tue Nov 19 15:39:55 CST 2013 -Built by: CTK@vpn-user-1-38.itc.virginia.edu [CMAKE] -Build OS/arch: Darwin 13.0.0 x86_64 -Build CPU vendor: GenuineIntel -Build CPU brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Build CPU family: 6 Model: 58 Stepping: 9 -Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -C compiler: /usr/bin/gcc Clang Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1 -C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG - - - :-) G R O M A C S (-: - - Gyas ROwers Mature At Cryogenic Speed - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) mdrun (-: - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl -GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable -molecular simulation -J. Chem. Theory Comput. 4 (2008) pp. 435-447 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. -Berendsen -GROMACS: Fast, Flexible and Free -J. Comp. Chem. 26 (2005) pp. 1701-1719 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -E. Lindahl and B. Hess and D. van der Spoel -GROMACS 3.0: A package for molecular simulation and trajectory analysis -J. Mol. Mod. 7 (2001) pp. 306-317 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, D. van der Spoel and R. van Drunen -GROMACS: A message-passing parallel molecular dynamics implementation -Comp. Phys. Comm. 91 (1995) pp. 43-56 --------- -------- --- Thank You --- -------- -------- - -Input Parameters: - integrator = md-vv - nsteps = 0 - init-step = 0 - cutoff-scheme = Group - ns_type = Grid - nstlist = 10 - ndelta = 2 - nstcomm = 10 - comm-mode = Linear - nstlog = 1000 - nstxout = 1000 - nstvout = 1000 - nstfout = 0 - nstcalcenergy = 10 - nstenergy = 1000 - nstxtcout = 0 - init-t = 0 - delta-t = 0.002 - xtcprec = 1000 - fourierspacing = 0.12 - nkx = 28 - nky = 28 - nkz = 28 - pme-order = 4 - ewald-rtol = 1e-06 - ewald-geometry = 0 - epsilon-surface = 0 - optimize-fft = FALSE - ePBC = xyz - bPeriodicMols = FALSE - bContinuation = FALSE - bShakeSOR = FALSE - etc = Berendsen - bPrintNHChains = FALSE - nsttcouple = 1 - epc = Berendsen - epctype = Isotropic - nstpcouple = 1 - tau-p = 10 - ref-p (3x3): - ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} - ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} - ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} - compress (3x3): - compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} - compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} - compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} - refcoord-scaling = No - posres-com (3): - posres-com[0]= 0.00000e+00 - posres-com[1]= 0.00000e+00 - posres-com[2]= 0.00000e+00 - posres-comB (3): - posres-comB[0]= 0.00000e+00 - posres-comB[1]= 0.00000e+00 - posres-comB[2]= 0.00000e+00 - verlet-buffer-drift = 0.005 - rlist = 1.5 - rlistlong = 1.5 - nstcalclr = 0 - rtpi = 0.05 - coulombtype = PME - coulomb-modifier = None - rcoulomb-switch = 0 - rcoulomb = 1.5 - vdwtype = Switch - vdw-modifier = None - rvdw-switch = 1.2 - rvdw = 1.25 - epsilon-r = 1 - epsilon-rf = inf - tabext = 1 - implicit-solvent = No - gb-algorithm = Still - gb-epsilon-solvent = 80 - nstgbradii = 1 - rgbradii = 1 - gb-saltconc = 0 - gb-obc-alpha = 1 - gb-obc-beta = 0.8 - gb-obc-gamma = 4.85 - gb-dielectric-offset = 0.009 - sa-algorithm = Ace-approximation - sa-surface-tension = 2.05016 - DispCorr = AllEnerPres - bSimTemp = FALSE - free-energy = no - nwall = 0 - wall-type = 9-3 - wall-atomtype[0] = -1 - wall-atomtype[1] = -1 - wall-density[0] = 0 - wall-density[1] = 0 - wall-ewald-zfac = 3 - pull = no - rotation = FALSE - disre = No - disre-weighting = Conservative - disre-mixed = FALSE - dr-fc = 1000 - dr-tau = 0 - nstdisreout = 100 - orires-fc = 0 - orires-tau = 0 - nstorireout = 100 - dihre-fc = 0 - em-stepsize = 0.01 - em-tol = 10 - niter = 20 - fc-stepsize = 0 - nstcgsteep = 1000 - nbfgscorr = 10 - ConstAlg = Lincs - shake-tol = 0.0001 - lincs-order = 4 - lincs-warnangle = 30 - lincs-iter = 1 - bd-fric = 0 - ld-seed = 1993 - cos-accel = 0 - deform (3x3): - deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - adress = FALSE - userint1 = 0 - userint2 = 0 - userint3 = 0 - userint4 = 0 - userreal1 = 0 - userreal2 = 0 - userreal3 = 0 - userreal4 = 0 -grpopts: - nrdf: 24 - ref-t: 300 - tau-t: 10 -anneal: No -ann-npoints: 0 - acc: 0 0 0 - nfreeze: N N N - energygrp-flags[ 0]: 0 - efield-x: - n = 0 - efield-xt: - n = 0 - efield-y: - n = 0 - efield-yt: - n = 0 - efield-z: - n = 0 - efield-zt: - n = 0 - bQMMM = FALSE - QMconstraints = 0 - QMMMscheme = 0 - scalefactor = 1 -qm-opts: - ngQM = 0 -Using 1 MPI thread - -Detecting CPU-specific acceleration. -Present hardware specification: -Vendor: GenuineIntel -Brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Family: 6 Model: 58 Stepping: 9 -Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -Acceleration most likely to fit this hardware: AVX_256 -Acceleration selected at GROMACS compile time: AVX_256 - -Table routines are used for coulomb: FALSE -Table routines are used for vdw: TRUE -Will do PME sum in reciprocal space. - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen -A smooth particle mesh Ewald method -J. Chem. Phys. 103 (1995) pp. 8577-8592 --------- -------- --- Thank You --- -------- -------- - -Will do ordinary reciprocal space Ewald sum. -Using a Gaussian width (1/beta) of 0.433663 nm for Ewald -Using shifted Lennard-Jones, switch between 1.2 and 1.25 nm -Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.25 -Long Range LJ corr.: 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:52:45 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Angle Proper Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.63616e+01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 4.35817e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 6.93858e+01 2.58625e+02 -2.66312e-11 5.76132e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Angle Proper Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.63616e+01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 4.35817e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 6.93858e+01 2.58625e+02 -2.66312e-11 5.76132e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -7.84062e+01 1.78548e+01 -2.76388e+01 - 1.78552e+01 -1.65019e+01 -3.25615e+01 - -2.76388e+01 -3.25619e+01 1.06511e+02 - - Pressure (bar) - 1.06217e+02 -2.22123e+01 3.05823e+01 - -2.22127e+01 2.95802e+01 4.11974e+01 - 3.05824e+01 4.11979e+01 -1.18513e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - Propers 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 7.8 - Force 1 1 1 0.000 0.000 4.5 - PME mesh 1 1 1 0.001 0.002 48.6 - Write traj. 1 1 1 0.000 0.001 25.2 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 13.5 ------------------------------------------------------------------------------ - Total 1 0.002 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 4.8 - PME 3D-FFT 1 1 2 0.000 0.001 21.4 - PME solve 1 1 1 0.000 0.001 21.5 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.8 - (ns/day) (hour/ns) -Performance: 98.569 0.243 -Finished mdrun on node 0 Fri Jun 20 15:52:45 2014 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral1/mdout.mdp b/testing/inputs/Gromacs/UnitTest/dihedral1/mdout.mdp deleted file mode 100644 index 321d336e..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral1/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/dihedral1/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:45 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral1/topol.tpr b/testing/inputs/Gromacs/UnitTest/dihedral1/topol.tpr deleted file mode 100644 index 93330296b3a3de7655ad49f35dce6d805d03fae5..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4128 zcmdT{YfPJE6n?oQgNY37hLbdS--G}y<<|Cl+YdtVvIbcAp;0$N30V*js>z6Gr_sO& zPMz5V{jsQjjM-+gEJI~&orz8}rkFTF7DM>6sF}gVm>DDLdA@$9d#xjdY>DwCPtX0l z=e@QSLaY};quyZg#qPT&O0>LE6Dqv2L z^6)v+Z?I%Kg0zqk8vjVtRGMMaXR1Js1o;K@!P?41cgYFkq;$*nz-ckW}=HK5rwGTq7v`ACyB{A_~Y> z%#ioQ;x%IR83lI7(D3_psi$l0$9fm)ExyZ+=8p}&Nttw;-1W(5wQup48Rp)( ziAjBLL0_Do7earn|6MQh@4CA5w=Q&fnZrJ7vl)KydD1TwPsMpZ-GO6dH#zm6R{J{5 zIX^VcJaJAnp^=tK0(0`?E@F?3d+L#;>)nMzi_8=A|02@%WZvm|>eN2wW{vnAUu}%% zx#h7)*}R20)k!sB49j)g=h8P}EO2t*o&W|R2EB%BS}rnYA9JpAJ$mLjGp8~5EsOU< z0?zb0LM|bXfOqpoLO$Up0?s({crLh`xRa_4K2={ShTm5!#pC_O7$D@bjCIAhAk@Y9 zAk^GIfDLyX@vz}NU>SX}jB~OY!aIn2i5@^0|7HT~7!U6+>lhP$#DUn)I{X&X4nK6v z6~w)x9*Fx_b<9E4F%R@-ynDpqS9SKoj(W-F?W7o-O`Z?;1RKvmwV@_RwQ(-@uhxSN zy(HSumpX=;%j2rKs*Q8e14zwPZ9J}OOST@didR1GAhC#m8d!6dQJZDdyp@1+h+ZIL zO`vZ!W#qDqT$VW(^W%8P91oe}A+NQ6O8H+A?-e-K5^n_X009IUZvfU9d$War-v#vq zoxpKef2)nbJAdAZ?uw%hDZQ>8R3V`M?MA?w&E}THh`m zQ?1e#oR%(aSk~pXFybBa7D>Meq+ZY`w_g5AR{0lX!^Zvc-qC7#-;C^tl) z{^XlBn{z{O8g`sF*RQAck%;$|kzVyu^-0nbNj-CM*<+2>R)f{CVTWGh40ot8$#gXq za?R`s{4NlhmKOlt1N|rSc_MP7yPLq 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:52:51 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Angle Improper Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 2.48592e+01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 5.20793e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 7.78834e+01 2.58625e+02 -2.66312e-11 5.76151e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Angle Improper Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 2.48592e+01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 5.20793e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 7.78834e+01 2.58625e+02 -2.66312e-11 5.76151e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -7.75168e+01 1.86503e+01 -2.92092e+01 - 1.86504e+01 -1.83393e+01 -3.35774e+01 - -2.92088e+01 -3.35775e+01 1.07458e+02 - - Pressure (bar) - 1.05135e+02 -2.31803e+01 3.24936e+01 - -2.31805e+01 3.18164e+01 4.24338e+01 - 3.24931e+01 4.24339e+01 -1.19666e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - Impropers 0.000012 0.002 0.0 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 6.3 - Force 1 1 1 0.000 0.000 4.2 - PME mesh 1 1 1 0.001 0.002 48.6 - Write traj. 1 1 1 0.000 0.001 25.6 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 14.9 ------------------------------------------------------------------------------ - Total 1 0.002 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.0 - PME 3D-FFT 1 1 2 0.000 0.001 21.6 - PME solve 1 1 1 0.000 0.001 21.2 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 113.017 0.212 -Finished mdrun on node 0 Fri Jun 20 15:52:51 2014 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral2/mdout.mdp b/testing/inputs/Gromacs/UnitTest/dihedral2/mdout.mdp deleted file mode 100644 index bfff7467..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral2/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/dihedral2/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:45 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral2/topol.tpr b/testing/inputs/Gromacs/UnitTest/dihedral2/topol.tpr deleted file mode 100644 index 951f9a4fcd24a41168aff7fc3dc7cea1122c1f62..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4124 zcmdT{YfPJE6n?oQ14M>)!$}&vZ$f~Ua%=m&?FXTFSpzKm(5M@sge(XXs>z6Gr_sO& z&RaG?e=M7SjM-+gEJI~&orz8}rkFTF7DM>6sF}gVm>DDLdA@$9zSa>+w#0anhjTyg zd9Pm)LgWh}@;aK@+FSfvt@d(9xs41&>4bK|20}I=Yaq}Y*fAI&QQSaCfnXA36)>kr zdE~t5H`r=Ag0zqk8vm21#~oJ}ZXt6TAywaI1fb9C{$0I;k5}5N+2_*}efA3W`F)AL zYCHRU{(t#U(^#9PV9$=e{$2!N-O`%28HHlKcwvs&ecnn%u8Pb4X2q_^db1IefqY+c z6@plXgJo=479q2J_h2ya1W6%>T_jZj~7^fUV_p>g(e zJlh+#EMIn%20vo|YTUKZ(B<2ENicU8bZ+%M9~E)F>D5`^BPo+^le<11t?@1XJj2{O zH!-R2E$ol;3qt6x?Rv+{{M+ts{q2k0UgogR+H8g&e4g}+B~#3GI&IoFEH)1Ssa^Q{t1|bH$hHG0dF=rohu5&$l<~cK`G58&e_d^2C z^EyHM0eL(Z+)La?)drucuN1>?tCiyM_F@bWa#_Z@Vq6gFVtf#4 zt|!2T`;B{){(|IQ**4e%Mhj*?Ci_a1wA%d2ZYvY&;*;hWa4Y#<@HfwH|Ef zE767?)iKmu9#_p(ZJdi9Kx(dP<8f76GHY`O)hs3;4{Odc>amPEw-Rs;F+OCh1N2R% zj9iwH%QEL;P8<)J;~{fAURb{(xgG@kRg-5I~Ue24Ib`H=7CgP0&El2^@#@ z$9ka-?+exxYsqW)U&l}@#yMF_pM1Von#WrGd|$z_woH)IBOxKy0(`GjS}m6cBd+#= zJ%fHN9D9!M1Kvi=1#fgxB+K?>O6ORkv~@i!%eH%^qgs;{1Mkbbd&i_Jze75v+N3Qw zEnV8Mtk1n)*1k|^#5?9Kl716Ny|7o~_AkiB4X?|4M{DGLXJ=$f^HEvebVzRQ zdsBK{Ps+OvjJwVicZ4Ht)9zEstQTM3>`@?^HlNb5*#ZSUh7rt_r>^>uNmPR8_>vK`P z?1xC@3Ell$@nU4-&U4D-@r_R;thZ{1oa%b;?9AWxwC`w32#90Z(8^N_(Urz5M5$`J_z51n^Q=})7dgkJ?#~Q1x2CHMk4!zbH?o?w|)74nWwX-Mj zyFlQ+M1F#FRZ5XjA>6b!rngFs(mt2~v5)7Vh6wC|NnI=u?{eNgm*cU7H0W oX1%P>*>RmY_X}>o6QxIdzYrcPS=K< 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:52:57 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.74015e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.32056e+01 2.58625e+02 -2.66312e-11 5.76142e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.81392e-01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 2.74015e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 5.32056e+01 2.58625e+02 -2.66312e-11 5.76142e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -7.61061e+01 2.02645e+01 -2.79015e+01 - 2.02646e+01 -1.87161e+01 -3.56389e+01 - -2.79014e+01 -3.56392e+01 1.06425e+02 - - Pressure (bar) - 1.03418e+02 -2.51450e+01 3.09020e+01 - -2.51451e+01 3.22750e+01 4.49428e+01 - 3.09019e+01 4.49432e+01 -1.18408e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - RB-Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 6.7 - Force 1 1 1 0.000 0.000 4.6 - PME mesh 1 1 1 0.001 0.002 51.4 - Write traj. 1 1 1 0.000 0.001 22.7 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.000 14.2 ------------------------------------------------------------------------------ - Total 1 0.001 0.003 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 5.3 - PME 3D-FFT 1 1 2 0.000 0.001 22.6 - PME solve 1 1 1 0.000 0.001 22.7 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.001 0.001 99.9 - (ns/day) (hour/ns) -Performance: 119.167 0.201 -Finished mdrun on node 0 Fri Jun 20 15:52:57 2014 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral3/mdout.mdp b/testing/inputs/Gromacs/UnitTest/dihedral3/mdout.mdp deleted file mode 100644 index 3ee50fd0..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral3/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/dihedral3/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:45 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral3/topol.tpr b/testing/inputs/Gromacs/UnitTest/dihedral3/topol.tpr deleted file mode 100644 index 016a4c10864245ab9a21d2f0325aa2d9a49f45e2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4312 zcmdT{eN0!<}hVaj#%M4o#nIYmlzt^66SJzOSiSZ;q&N;tx z&b{Z}``&#;QIvE=QPP^K8yaitHXBR@<^m%TB=Lks!a71SA*tKl?%v+xCR4eA5CbD9 zuw{Ub5n}(DU|d%#`AAZ|dTQuTxE~5!+qi}3I6|y*i=Kc!lRLZGd$txCOE~6ohQ~~W z9IJDM$4X2bbJhJVhB5WMsrIyO@91nt0`@JgdW$|#pce<|0Pk`XNp^9_uB(xF$#&N0 zISHtD)f6L%Z3NiHktGol8+Z12+)tB5HX)(T)8_8h-9T=)yT?N=dPbiHLf&k#(_YE@E|37IByZ{J51u_wz-pLWbuX1gw%Yma0FG8BdRa;3lCNT|p< z@RjLx?-0j1pZUs7%a_b~o}(OJNn7VCTU@&@D6DN6&6`~>`IV5~@W!<3v6xX?P+N}= zl)C1Bonq~n85wo%&g=~7vx?$;v+I2a>mOTNo$sD&b+86MZ8Yj}=vng5&{`z79YvOT-;Mvsg7rV$$w`KLtv*tS1S4h-diFa9_ zJ+X&1#rPi5)1u9>zqmZ870hO{rsCKjt{TU7CVoBUf~El8Z$KB!g(&{$(F)kbSHJ{pt5LX~bopr^%-^Oxm75l&tPg>=V_!ZR!(0 zAJ+1|+@Y;mDAc+azOh*zKj<^`zhFB!pW@Hz|3z(BcB-#sr}_%B2W-cN_xk?$Ax-=3 zl`nh~XTP)M?mQ_{76!EEoHKrB{&}tFkkhu5Gq0`RaavkDzVYFL{g!#yvDSx9P5s5k z{X|DXKpxw=PZVo1Nz`r44}X8@gWs!q>BStMNm2d85rTqq#WT+w=8jcIMn=^!uu7cj z)wTTpT?})GIL4^fOQ8P5J4T~rt!ENEo;T~_i9KZE&S%7zyjpsU{BV(^kMuiQ1HHJ7hzpfVuW8&Y_vDQXtA87em(->7_UK2QE&!9 zX<>tOi{*})6uTkB;5}i9w+H$Oj+gW`2mWQv{X*-o`{@$jt0;B@F{==qJKsB8CInlN HHJ|IBodE{1 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral4/confout.gro b/testing/inputs/Gromacs/UnitTest/dihedral4/confout.gro deleted file mode 100644 index e42c8e99..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral4/confout.gro +++ /dev/null @@ -1,12 +0,0 @@ -Ethanol - 9 - 1ETH CB 1 2.711 2.946 2.803 0.1006 -0.3737 0.2468 - 1ETH HB1 2 2.709 2.847 2.757 1.3518 3.0856 0.8708 - 1ETH HB2 3 2.616 2.954 2.855 -0.6358 -0.5466 -0.9490 - 1ETH OG1 4 2.804 2.957 2.907 0.1840 -0.1568 0.3435 - 1ETH HG1 5 2.883 2.946 2.857 -2.3209 0.8242 1.1101 - 1ETH CG2 6 2.732 3.048 2.687 -0.1720 0.3703 -0.4977 - 1ETH HG21 7 2.833 3.064 2.649 -1.9416 -0.3611 0.1548 - 1ETH HG22 8 2.700 3.145 2.723 2.1709 -0.9620 -3.0497 - 1ETH HG23 9 2.663 3.035 2.603 -0.6942 0.4885 -0.5993 - 3.01061 3.01061 3.01061 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral4/gromacs_stderr.txt b/testing/inputs/Gromacs/UnitTest/dihedral4/gromacs_stderr.txt deleted file mode 100644 index b09c8fbc..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral4/gromacs_stderr.txt +++ /dev/null @@ -1,113 +0,0 @@ - :-) G R O M A C S (-: - - Gnomes, ROck Monsters And Chili Sauce - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) grompp (-: - -Option Filename Type Description ------------------------------------------------------------- - -f inputs/Gromacs/grompp.mdp Input grompp input file with MD - parameters - -po ./inputs/Gromacs/UnitTest/dihedral4/mdout.mdp Output grompp input - file with MD parameters - -c ./inputs/Gromacs/UnitTest/dihedral4/dihedral4.gro Input - Structure file: gro g96 pdb tpr etc. - -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. - -n index.ndx Input, Opt. Index file - -p ./inputs/Gromacs/UnitTest/dihedral4/dihedral4.top Input Topology - file - -pp processed.top Output, Opt. Topology file - -o ./inputs/Gromacs/UnitTest/dihedral4/topol.tpr Output Run input - file: tpr tpb tpa - -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt - -e ener.edr Input, Opt. Energy file --ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt - -Option Type Value Description ------------------------------------------------------- --[no]h bool no Print help info and quit --[no]version bool no Print version info and quit --nice int 0 Set the nicelevel --[no]v bool no Be loud and noisy --time real -1 Take frame at or first after this time. --[no]rmvsbds bool yes Remove constant bonded interactions with virtual - sites --maxwarn int 1 Number of allowed warnings during input - processing. Not for normal use and may generate - unstable systems --[no]zero bool no Set parameters for bonded interactions without - defaults to zero instead of generating an error --[no]renum bool yes Renumber atomtypes and minimize number of - atomtypes - - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/dihedral4/mdout.mdp to ./inputs/Gromacs/UnitTest/dihedral4/#mdout.mdp.25# - -NOTE 1 [file inputs/Gromacs/grompp.mdp]: - nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting - nstcomm to nstcalcenergy - - -NOTE 2 [file inputs/Gromacs/grompp.mdp]: - The Berendsen thermostat does not generate the correct kinetic energy - distribution. You might want to consider using the V-rescale thermostat. - - -NOTE 3 [file inputs/Gromacs/grompp.mdp]: - The switch/shift interaction settings are just for compatibility; you - will get better performance from applying potential modifiers to your - interactions! - - -Generated 10 of the 10 non-bonded parameter combinations -Generating 1-4 interactions: fudge = 0.5 -Generated 10 of the 10 1-4 parameter combinations -Excluding 3 bonded neighbours molecule type 'Ethanol' -Velocities were taken from a Maxwell distribution at 300 K - -WARNING 1 [file dihedral4.top, line 111]: - The bond in molecule-type Ethanol between atoms 4 OG1 and 5 HG1 has an - estimated oscillational period of 9.0e-03 ps, which is less than 5 times - the time step of 2.0e-03 ps. - Maybe you forgot to change the constraints mdp option. - -Number of degrees of freedom in T-Coupling group System is 24.00 -Estimate for the relative computational load of the PME mesh part: 0.99 - -NOTE 4 [file inputs/Gromacs/grompp.mdp]: - The optimal PME mesh load for parallel simulations is below 0.5 - and for highly parallel simulations between 0.25 and 0.33, - for higher performance, increase the cut-off and the PME grid spacing. - - - -There were 4 notes - -There was 1 warning - -Back Off! I just backed up ./inputs/Gromacs/UnitTest/dihedral4/topol.tpr to ./inputs/Gromacs/UnitTest/dihedral4/#topol.tpr.25# - -gcq#155: "Shake Yourself" (YES) - diff --git a/testing/inputs/Gromacs/UnitTest/dihedral4/gromacs_stdout.txt b/testing/inputs/Gromacs/UnitTest/dihedral4/gromacs_stdout.txt deleted file mode 100644 index bae942ca..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral4/gromacs_stdout.txt +++ /dev/null @@ -1,8 +0,0 @@ -Analysing residue names: -There are: 1 Other residues -Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -Largest charge group radii for Van der Waals: 0.103, 0.101 nm -Largest charge group radii for Coulomb: 0.103, 0.101 nm -Calculating fourier grid dimensions for X Y Z -Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -This run will generate roughly 0 Mb of data diff --git a/testing/inputs/Gromacs/UnitTest/dihedral4/md.log b/testing/inputs/Gromacs/UnitTest/dihedral4/md.log deleted file mode 100644 index 7aa08b86..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral4/md.log +++ /dev/null @@ -1,401 +0,0 @@ -Log file opened on Fri Jun 20 15:53:03 2014 -Host: Christophs-MacBook-Air.local pid: 23393 nodeid: 0 nnodes: 1 -Gromacs version: VERSION 4.6.3 -Precision: single -Memory model: 64 bit -MPI library: thread_mpi -OpenMP support: disabled -GPU support: disabled -invsqrt routine: gmx_software_invsqrt(x) -CPU acceleration: AVX_256 -FFT library: fftw-3.3.2-sse2 -Large file support: enabled -RDTSCP usage: enabled -Built on: Tue Nov 19 15:39:55 CST 2013 -Built by: CTK@vpn-user-1-38.itc.virginia.edu [CMAKE] -Build OS/arch: Darwin 13.0.0 x86_64 -Build CPU vendor: GenuineIntel -Build CPU brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Build CPU family: 6 Model: 58 Stepping: 9 -Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -C compiler: /usr/bin/gcc Clang Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1 -C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG - - - :-) G R O M A C S (-: - - Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm - - :-) VERSION 4.6.3 (-: - - Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, - Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, - Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, - Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, - Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, - Michael Shirts, Alfons Sijbers, Peter Tieleman, - - Berk Hess, David van der Spoel, and Erik Lindahl. - - Copyright (c) 1991-2000, University of Groningen, The Netherlands. - Copyright (c) 2001-2012,2013, The GROMACS development team at - Uppsala University & The Royal Institute of Technology, Sweden. - check out http://www.gromacs.org for more information. - - This program is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public License - as published by the Free Software Foundation; either version 2.1 - of the License, or (at your option) any later version. - - :-) mdrun (-: - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl -GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable -molecular simulation -J. Chem. Theory Comput. 4 (2008) pp. 435-447 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. -Berendsen -GROMACS: Fast, Flexible and Free -J. Comp. Chem. 26 (2005) pp. 1701-1719 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -E. Lindahl and B. Hess and D. van der Spoel -GROMACS 3.0: A package for molecular simulation and trajectory analysis -J. Mol. Mod. 7 (2001) pp. 306-317 --------- -------- --- Thank You --- -------- -------- - - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, D. van der Spoel and R. van Drunen -GROMACS: A message-passing parallel molecular dynamics implementation -Comp. Phys. Comm. 91 (1995) pp. 43-56 --------- -------- --- Thank You --- -------- -------- - -Input Parameters: - integrator = md-vv - nsteps = 0 - init-step = 0 - cutoff-scheme = Group - ns_type = Grid - nstlist = 10 - ndelta = 2 - nstcomm = 10 - comm-mode = Linear - nstlog = 1000 - nstxout = 1000 - nstvout = 1000 - nstfout = 0 - nstcalcenergy = 10 - nstenergy = 1000 - nstxtcout = 0 - init-t = 0 - delta-t = 0.002 - xtcprec = 1000 - fourierspacing = 0.12 - nkx = 28 - nky = 28 - nkz = 28 - pme-order = 4 - ewald-rtol = 1e-06 - ewald-geometry = 0 - epsilon-surface = 0 - optimize-fft = FALSE - ePBC = xyz - bPeriodicMols = FALSE - bContinuation = FALSE - bShakeSOR = FALSE - etc = Berendsen - bPrintNHChains = FALSE - nsttcouple = 1 - epc = Berendsen - epctype = Isotropic - nstpcouple = 1 - tau-p = 10 - ref-p (3x3): - ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} - ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} - ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} - compress (3x3): - compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} - compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} - compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} - refcoord-scaling = No - posres-com (3): - posres-com[0]= 0.00000e+00 - posres-com[1]= 0.00000e+00 - posres-com[2]= 0.00000e+00 - posres-comB (3): - posres-comB[0]= 0.00000e+00 - posres-comB[1]= 0.00000e+00 - posres-comB[2]= 0.00000e+00 - verlet-buffer-drift = 0.005 - rlist = 1.5 - rlistlong = 1.5 - nstcalclr = 0 - rtpi = 0.05 - coulombtype = PME - coulomb-modifier = None - rcoulomb-switch = 0 - rcoulomb = 1.5 - vdwtype = Switch - vdw-modifier = None - rvdw-switch = 1.2 - rvdw = 1.25 - epsilon-r = 1 - epsilon-rf = inf - tabext = 1 - implicit-solvent = No - gb-algorithm = Still - gb-epsilon-solvent = 80 - nstgbradii = 1 - rgbradii = 1 - gb-saltconc = 0 - gb-obc-alpha = 1 - gb-obc-beta = 0.8 - gb-obc-gamma = 4.85 - gb-dielectric-offset = 0.009 - sa-algorithm = Ace-approximation - sa-surface-tension = 2.05016 - DispCorr = AllEnerPres - bSimTemp = FALSE - free-energy = no - nwall = 0 - wall-type = 9-3 - wall-atomtype[0] = -1 - wall-atomtype[1] = -1 - wall-density[0] = 0 - wall-density[1] = 0 - wall-ewald-zfac = 3 - pull = no - rotation = FALSE - disre = No - disre-weighting = Conservative - disre-mixed = FALSE - dr-fc = 1000 - dr-tau = 0 - nstdisreout = 100 - orires-fc = 0 - orires-tau = 0 - nstorireout = 100 - dihre-fc = 0 - em-stepsize = 0.01 - em-tol = 10 - niter = 20 - fc-stepsize = 0 - nstcgsteep = 1000 - nbfgscorr = 10 - ConstAlg = Lincs - shake-tol = 0.0001 - lincs-order = 4 - lincs-warnangle = 30 - lincs-iter = 1 - bd-fric = 0 - ld-seed = 1993 - cos-accel = 0 - deform (3x3): - deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} - adress = FALSE - userint1 = 0 - userint2 = 0 - userint3 = 0 - userint4 = 0 - userreal1 = 0 - userreal2 = 0 - userreal3 = 0 - userreal4 = 0 -grpopts: - nrdf: 24 - ref-t: 300 - tau-t: 10 -anneal: No -ann-npoints: 0 - acc: 0 0 0 - nfreeze: N N N - energygrp-flags[ 0]: 0 - efield-x: - n = 0 - efield-xt: - n = 0 - efield-y: - n = 0 - efield-yt: - n = 0 - efield-z: - n = 0 - efield-zt: - n = 0 - bQMMM = FALSE - QMconstraints = 0 - QMMMscheme = 0 - scalefactor = 1 -qm-opts: - ngQM = 0 -Using 1 MPI thread - -Detecting CPU-specific acceleration. -Present hardware specification: -Vendor: GenuineIntel -Brand: Intel(R) Core(TM) i5-3427U CPU @ 1.80GHz -Family: 6 Model: 58 Stepping: 9 -Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -Acceleration most likely to fit this hardware: AVX_256 -Acceleration selected at GROMACS compile time: AVX_256 - -Table routines are used for coulomb: FALSE -Table routines are used for vdw: TRUE -Will do PME sum in reciprocal space. - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen -A smooth particle mesh Ewald method -J. Chem. Phys. 103 (1995) pp. 8577-8592 --------- -------- --- Thank You --- -------- -------- - -Will do ordinary reciprocal space Ewald sum. -Using a Gaussian width (1/beta) of 0.433663 nm for Ewald -Using shifted Lennard-Jones, switch between 1.2 and 1.25 nm -Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.25 -Long Range LJ corr.: 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:53:03 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Angle Improper Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.16868e+02 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 1.44088e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 1.69893e+02 2.58625e+02 -2.66312e-11 5.76137e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Angle Improper Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.16868e+02 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 1.44088e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 1.69893e+02 2.58625e+02 -2.66312e-11 5.76137e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -7.86608e+01 1.22737e+01 -2.05492e+01 - 1.22736e+01 -1.30245e+01 -2.47440e+01 - -2.05490e+01 -2.47442e+01 1.03288e+02 - - Pressure (bar) - 1.06527e+02 -1.54196e+01 2.19538e+01 - -1.54195e+01 2.53479e+01 3.16830e+01 - 2.19536e+01 3.16832e+01 -1.14591e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - Impropers 0.000012 0.002 0.0 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 6.7 - Force 1 1 1 0.000 0.000 3.8 - PME mesh 1 1 1 0.001 0.003 51.4 - Write traj. 1 1 1 0.001 0.002 26.9 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 10.9 ------------------------------------------------------------------------------ - Total 1 0.002 0.006 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 4.9 - PME 3D-FFT 1 1 2 0.001 0.002 25.9 - PME solve 1 1 1 0.000 0.001 19.8 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 69.757 0.344 -Finished mdrun on node 0 Fri Jun 20 15:53:03 2014 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral4/mdout.mdp b/testing/inputs/Gromacs/UnitTest/dihedral4/mdout.mdp deleted file mode 100644 index fc095122..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral4/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/dihedral4/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:45 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral4/topol.tpr b/testing/inputs/Gromacs/UnitTest/dihedral4/topol.tpr deleted file mode 100644 index c787890a92f5efb03870c65524b3d2f7ec7d5fc4..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4128 zcmdT{YfPJE6n?oQ14M>)!$}&vZ$f~Ua%=m&?FXTFSpzKm(5M@sge(XM)nr7p(`aA> zr_OAG{#evM#%wb&%TQTcXQI=LDJG7P#Ss21YG!aTX2ytmp0D4juXUu5EisAAn> zyw|ouhw~>J;ozPC$M93y&4F-AxyM_WJit7j|5KMxs0_GGc zkDN3821}+RNDCRE@sC73?zpmW6PeQpsrn8h0DWfn5A+T_T4}3hpHENp*(=!R_a*wO z?ds=Ib}%p$Bo#fQ&szwkR|!i02j!5K2<%G< zL*5mO*N8P_6xtobBk$Iyp02aM-?!Lc@m+Sbd{`8V5Q6P>Vzkvps4qJDnf;~E1p7Ij z?G4*jE;&krAF)3fcP%z_`Sx8D%-sc@+kMYQMVxPWdCvDx%9PvWu8+rRd`myiGWX6; zPU-s!`{Vq)5c(?vZ+n@4+ug0daiQDG9QHYz&G3USkba?LI?e}#@K}ZLnwe6trwZIk2#NXEqdlTGp8E-mc{!a z0cUyxA(xOxz`J=pp@47$p^$()o(t|K?xbpiPt{k8;rG=_@pykx1B6_bv972K!nmjp z!k8Ngu;Gp)9yYuOETb=$aZc7kcn5JW(E|weZzQmedbsDTqbB@_1F@fV_${U#e(0Dh zhu~4YpA(gSIt#zoQobnYOZSIx~eVN`rJn26%&wyHD?)Pv5YZpCg2>RHe{>; z^ev{0T$Yi`GUsAG91oe}A#*(BWc^ae|C)Gjz_FHiBY^t|Ajo(Fu*TS%tpxloXdvhW zj>Gz6y)X{%3)U2C$!qvu$51QAIayDie70Ac$9nyISHZEiOpwzfAtBZSd|#=QESHNB zSNp)8LBAS~J;(P0-bTy?Z}gf-mhH`y&hbWR>v~X@?et1VwI(YD-;;Otj!Rd5hjdK0 zNn3D6y0j5lpL?&YeXh`mcPv;W{U(rlVZYpV`Ab>tUzClT4#>O5YUDj0-V$pQA;|MlcEciZjnP)K1kVC#ST-u!=M-WN`I=QVQGP@gAn!5P|xW zuiI?Sjlmh%ao$|NoZ3$!-d9F?^$Rs8Nlzs8%*ADoH8!>ytk#AddaX0usm3JJ)mX^2 zb0_e-K;XVaeu8vGN|8|^+_W~Pw@QuDK9~ftkLRF<2<(ALT`Umqa^5)KTcv+vb;~I1B7uva~wqef 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:53:09 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Angle Fourier Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.93114e+01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 4.65315e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 7.23356e+01 2.58625e+02 -2.66312e-11 5.76139e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Angle Fourier Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.93114e+01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 4.65315e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 7.23356e+01 2.58625e+02 -2.66312e-11 5.76139e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -7.77793e+01 1.93504e+01 -2.83243e+01 - 1.93505e+01 -1.78401e+01 -3.38016e+01 - -2.83245e+01 -3.38020e+01 1.07222e+02 - - Pressure (bar) - 1.05454e+02 -2.40325e+01 3.14167e+01 - -2.40326e+01 3.12089e+01 4.27067e+01 - 3.14169e+01 4.27072e+01 -1.19379e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - Four. Dihedrals 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 5.8 - Force 1 1 1 0.000 0.000 4.1 - PME mesh 1 1 1 0.001 0.002 51.3 - Write traj. 1 1 1 0.000 0.001 24.4 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 13.9 ------------------------------------------------------------------------------ - Total 1 0.002 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 4.7 - PME 3D-FFT 1 1 2 0.000 0.001 22.2 - PME solve 1 1 1 0.000 0.001 23.7 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 106.148 0.226 -Finished mdrun on node 0 Fri Jun 20 15:53:09 2014 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral5/mdout.mdp b/testing/inputs/Gromacs/UnitTest/dihedral5/mdout.mdp deleted file mode 100644 index 61d1252c..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral5/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/dihedral5/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:45 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral5/topol.tpr b/testing/inputs/Gromacs/UnitTest/dihedral5/topol.tpr deleted file mode 100644 index bdc7febad922a864b7caee45afd0e75dcc77fdb2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4156 zcmdT`YfPI}7(U#Q0U|@Y;Uo>-Hz7bvxwZXH`#~sP)&L7XH0nkuAq&EUYBD0)X*4i` z^OjA}AB+0Om~AFz87k{nXQI=LDJG7P#Ss21YG!aTX2yv6K41IRvkIX&6XTmayw7_( z=RN0q=TIR;z7Qg>qp7XE#lPKZFL#vN$U%}$XeVqUWD~Lm0=NVyZZWjk$`5gJ)_T?2&GpED!)Q<$Vx;J z`AQh_j%dC{sv)D$?id<=r#|&`o&CMOg$9f7vZLh#$rd=P6*7z2Gnqlpo zo0!!17xu^Xc_H+d_Ppg~{Y`hb{`!S(FKhT`Z8kFwJx}(9k}1}b8rDKWNFov95#kU@ zSjk`a3hhThXq+{2RjCb)v{n&VQw;YM=WpI&k1We~7Y!}4R%^lkAkp?^-s*bn)B)Dy z=DTjDC!6DWYI)2kpSQ54;?x+f7{`4seKY2QrU32`U<&3!ui@I(i>x`uI@x}BJ*=tz zAFYe(@V##!6cDZ>6cR8tuLbuO_f_>FrrN9J@Y`#pe7wz=1AS|_)d}$ypg!G=mCQHuP3mL`S3QgjX4oV9)#m;BW{WL z5r>VnLb!K~2jTuz8*5N)tONa-Zz5^LRh#4RW4vV7?WA0Mqr5Ke4L)9r>ciL&)yK8G z4s|^E&{Luh{i$=PwLGs{tNOSWJwVi2)yMOyzGV0178VqKgM&iUY+51wq_l={CEJ|k%CCEf_&9s&d$ZvgffXS0=n-wX`| zoxpk6f9w~=;d8;BVlR0Q|LYuT#r#gz(E0(82KUU*{RWJo|BY>in1PlD(&8&eEvy zxIP!r%f2@%kL&JVix-W}yU!|%$N%_5!G5cL@Ko2mXJ-ELr+rIDLO>pK(dq9oeR z&ilT)^!9I!Lv%6UoXgQ7}QWJ%Qf^=I>JDN3azoMMi{h)853QRce;@{se?$yaqKz;0$8Y#e{U1^X9o6k2UVW uJz+`rMEi-2m-QJ3{$ 1.2935e-11, -3.1580e-15 -System total charge: -0.000 -Generated table with 1250 data points for Ewald. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ6Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for LJ12Switch. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 COUL. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ6. -Tabscale = 500 points/nm -Generated table with 1250 data points for 1-4 LJ12. -Tabscale = 500 points/nm -Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 -Initialized non-bonded Ewald correction tables, spacing: 7.68e-04 size: 3257 - -Removing pbc first time -Center of mass motion removal mode is Linear -We have the following groups for center of mass motion removal: - 0: rest - -++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak -Molecular dynamics with coupling to an external bath -J. Chem. Phys. 81 (1984) pp. 3684-3690 --------- -------- --- Thank You --- -------- -------- - -There are: 9 Atoms -Max number of connections per atom is 44 -Total number of connections is 164 -Max number of graph edges per atom is 4 -Total number of graph edges is 16 -Initial temperature: 258.625 K - -Started mdrun on node 0 Fri Jun 20 15:53:16 2014 - - Step Time Lambda - 0 0.00000 0.00000 - - -Grid: 2 x 2 x 2 cells - Energies (kJ/mol) - Bond Angle Proper Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.54074e+01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 4.26275e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 6.84317e+01 2.58625e+02 -2.66312e-11 5.76160e+00 - - <====== ############### ==> - <==== A V E R A G E S ====> - <== ############### ======> - - Statistics over 1 steps using 1 frames - - Energies (kJ/mol) - Bond Angle Proper Dih. LJ-14 Coulomb-14 - 1.31061e+00 2.01175e+01 1.54074e+01 -3.60990e-01 -2.96506e+01 - LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential - 0.00000e+00 -4.37628e-11 1.24006e+01 2.34031e+01 4.26275e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.58041e+01 6.84317e+01 2.58625e+02 -2.66312e-11 5.76160e+00 - - Box-X Box-Y Box-Z - 3.01061e+00 3.01061e+00 3.01061e+00 - - Total Virial (kJ/mol) - -8.19822e+01 1.89393e+01 -2.67234e+01 - 1.89392e+01 -1.46945e+01 -3.00296e+01 - -2.67233e+01 -3.00297e+01 1.08279e+02 - - Pressure (bar) - 1.10569e+02 -2.35321e+01 2.94682e+01 - -2.35320e+01 2.73805e+01 3.81158e+01 - 2.94681e+01 3.81160e+01 -1.20665e+02 - - - M E G A - F L O P S A C C O U N T I N G - - NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels - RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table - W3=SPC/TIP3p W4=TIP4p (single or pairs) - V&F=Potential and force V=Potential only F=Force only - - Computing: M-Number M-Flops % Flops ------------------------------------------------------------------------------ - NB Elec. [V&F] 0.000696 0.001 0.0 - 1,4 nonbonded interactions 0.000012 0.001 0.0 - Calc Weights 0.000027 0.001 0.0 - Spread Q Bspline 0.000576 0.001 0.0 - Gather F Bspline 0.000576 0.003 0.1 - 3D-FFT 0.633186 5.065 98.7 - Solve PME 0.000784 0.050 1.0 - NS-Pairs 0.000008 0.000 0.0 - Reset In Box 0.000003 0.000 0.0 - Shift-X 0.000018 0.000 0.0 - CG-CoM 0.000009 0.000 0.0 - Bonds 0.000008 0.000 0.0 - Angles 0.000013 0.002 0.0 - Propers 0.000012 0.003 0.1 - Virial 0.000054 0.001 0.0 - Stop-CM 0.000009 0.000 0.0 - P-Coupling 0.000009 0.000 0.0 - Calc-Ekin 0.000009 0.000 0.0 ------------------------------------------------------------------------------ - Total 5.130 100.0 ------------------------------------------------------------------------------ - - - R E A L C Y C L E A N D T I M E A C C O U N T I N G - - Computing: Nodes Th. Count Wall t (s) G-Cycles % ------------------------------------------------------------------------------ - Neighbor search 1 1 1 0.000 0.000 6.0 - Force 1 1 1 0.000 0.000 3.8 - PME mesh 1 1 1 0.001 0.002 47.5 - Write traj. 1 1 1 0.000 0.001 23.7 - Update 1 1 1 0.000 0.000 0.4 - Rest 1 0.000 0.001 18.7 ------------------------------------------------------------------------------ - Total 1 0.002 0.004 100.0 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ - PME spread/gather 1 1 2 0.000 0.000 4.7 - PME 3D-FFT 1 1 2 0.000 0.001 22.2 - PME solve 1 1 1 0.000 0.001 19.8 ------------------------------------------------------------------------------ - - Core t (s) Wall t (s) (%) - Time: 0.002 0.002 99.9 - (ns/day) (hour/ns) -Performance: 100.817 0.238 -Finished mdrun on node 0 Fri Jun 20 15:53:16 2014 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral9/mdout.mdp b/testing/inputs/Gromacs/UnitTest/dihedral9/mdout.mdp deleted file mode 100644 index e7261621..00000000 --- a/testing/inputs/Gromacs/UnitTest/dihedral9/mdout.mdp +++ /dev/null @@ -1,343 +0,0 @@ -; -; File './inputs/Gromacs/UnitTest/dihedral9/mdout.mdp' was generated -; By user: CTK (501) -; On host: Christophs-MacBook-Air.local -; At date: Fri Jun 20 17:03:45 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; Preprocessor information: use cpp syntax. -; e.g.: -I/home/joe/doe -I/home/mary/roe -include = -; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) -define = - -; RUN CONTROL PARAMETERS -integrator = md-vv -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 0 -; For exact run continuation or redoing part of a run -init-step = 0 -; Part index is updated automatically on checkpointing (keeps files separate) -simulation-part = 1 -; mode for center of mass motion removal -comm-mode = Linear -; number of steps for center of mass motion removal -nstcomm = 1 -; group(s) for center of mass motion removal -comm-grps = - -; LANGEVIN DYNAMICS OPTIONS -; Friction coefficient (amu/ps) and random seed -bd-fric = 0 -ld-seed = 1993 - -; ENERGY MINIMIZATION OPTIONS -; Force tolerance and initial step-size -emtol = 10 -emstep = 0.01 -; Max number of iterations in relax-shells -niter = 20 -; Step size (ps^2) for minimization of flexible constraints -fcstep = 0 -; Frequency of steepest descents steps when doing CG -nstcgsteep = 1000 -nbfgscorr = 10 - -; TEST PARTICLE INSERTION OPTIONS -rtpi = 0.05 - -; OUTPUT CONTROL OPTIONS -; Output frequency for coords (x), velocities (v) and forces (f) -nstxout = 1000 -nstvout = 1000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 1000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 0 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -cutoff-scheme = Group -; nblist update frequency -nstlist = 10 -; ns algorithm (simple or grid) -ns_type = grid -; Periodic boundary conditions: xyz, no, xy -pbc = xyz -periodic-molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.005 -; nblist cut-off -rlist = 1.5 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = PME -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 1.5 -; Relative dielectric constant for the medium and the reaction field -epsilon-r = 1 -epsilon-rf = 0 -; Method for doing Van der Waals -vdw-type = switch -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 1.2 -rvdw = 1.25 -; Apply long range dispersion corrections for Energy and Pressure -DispCorr = AllEnerPres -; Extension of the potential lookup tables beyond the cut-off -table-extension = 1 -; Separate tables between energy group pairs -energygrp-table = -; Spacing for the PME/PPPM FFT grid -fourierspacing = 0.12 -; FFT grid size, when a value is 0 fourierspacing will be used -fourier_nx = 0 -fourier_ny = 0 -fourier_nz = 0 -; EWALD/PME/PPPM parameters -pme_order = 4 -ewald_rtol = 1e-06 -ewald_geometry = 3d -epsilon_surface = 0 -optimize_fft = no - -; IMPLICIT SOLVENT ALGORITHM -implicit-solvent = No - -; GENERALIZED BORN ELECTROSTATICS -; Algorithm for calculating Born radii -gb-algorithm = Still -; Frequency of calculating the Born radii inside rlist -nstgbradii = 1 -; Cutoff for Born radii calculation; the contribution from atoms -; between rlist and rgbradii is updated every nstlist steps -rgbradii = 1 -; Dielectric coefficient of the implicit solvent -gb-epsilon-solvent = 80 -; Salt concentration in M for Generalized Born models -gb-saltconc = 0 -; Scaling factors used in the OBC GB model. Default values are OBC(II) -gb-obc-alpha = 1 -gb-obc-beta = 0.8 -gb-obc-gamma = 4.85 -gb-dielectric-offset = 0.009 -sa-algorithm = Ace-approximation -; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA -; The value -1 will set default value for Still/HCT/OBC GB-models. -sa-surface-tension = -1 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -Tcoupl = berendsen -nsttcouple = 1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = System -; Time constant (ps) and reference temperature (K) -tau_t = 10.0 -ref_t = 300.0 -; pressure coupling -Pcoupl = berendsen -Pcoupltype = isotropic -nstpcouple = 1 -; Time constant (ps), compressibility (1/bar) and reference P (bar) -tau_p = 10.0 -compressibility = 4.5e-5 -ref_p = 1.0 -; Scaling of reference coordinates, No, All or COM -refcoord-scaling = No - -; OPTIONS FOR QMMM calculations -QMMM = no -; Groups treated Quantum Mechanically -QMMM-grps = -; QM method -QMmethod = -; QMMM scheme -QMMMscheme = normal -; QM basisset -QMbasis = -; QM charge -QMcharge = -; QM multiplicity -QMmult = -; Surface Hopping -SH = -; CAS space options -CASorbitals = -CASelectrons = -SAon = -SAoff = -SAsteps = -; Scale factor for MM charges -MMChargeScaleFactor = 1 -; Optimization of QM subsystem -bOPT = -bTS = - -; SIMULATED ANNEALING -; Type of annealing for each temperature group (no/single/periodic) -annealing = -; Number of time points to use for specifying annealing in each group -annealing-npoints = -; List of times at the annealing points for each group -annealing-time = -; Temp. at each annealing point, for each group. -annealing-temp = - -; GENERATE VELOCITIES FOR STARTUP RUN -gen_vel = yes -gen_temp = 300.0 -gen_seed = 4 - -; OPTIONS FOR BONDS -constraints = none -; Type of constraint algorithm -constraint-algorithm = Lincs -; Do not constrain the start configuration -continuation = no -; Use successive overrelaxation to reduce the number of shake iterations -Shake-SOR = no -; Relative tolerance of shake -shake-tol = 0.0001 -; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 -; Number of iterations in the final step of LINCS. 1 is fine for -; normal simulations, but use 2 to conserve energy in NVE runs. -; For energy minimization with constraints it should be 4 to 8. -lincs-iter = 1 -; Lincs will write a warning to the stderr if in one step a bond -; rotates over more degrees than -lincs-warnangle = 30 -; Convert harmonic bonds to morse potentials -morse = no - -; ENERGY GROUP EXCLUSIONS -; Pairs of energy groups for which all non-bonded interactions are excluded -energygrp-excl = - -; WALLS -; Number of walls, type, atom types, densities and box-z scale factor for Ewald -nwall = 0 -wall-type = 9-3 -wall-r-linpot = -1 -wall-atomtype = -wall-density = -wall-ewald-zfac = 3 - -; COM PULLING -; Pull type: no, umbrella, constraint or constant-force -pull = no - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = no - -; NMR refinement stuff -; Distance restraints type: No, Simple or Ensemble -disre = No -; Force weighting of pairs in one distance restraint: Conservative or Equal -disre-weighting = Conservative -; Use sqrt of the time averaged times the instantaneous violation -disre-mixed = no -disre-fc = 1000 -disre-tau = 0 -; Output frequency for pair distances to energy file -nstdisreout = 100 -; Orientation restraints: No or Yes -orire = no -; Orientation restraints force constant and tau for time averaging -orire-fc = 0 -orire-tau = 0 -orire-fitgrp = -; Output frequency for trace(SD) and S to energy file -nstorireout = 100 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = -1 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 50 -fep-lambdas = -mass-lambdas = -coul-lambdas = -vdw-lambdas = -bonded-lambdas = -restraint-lambdas = -temperature-lambdas = -calc-lambda-neighbors = 1 -init-lambda-weights = -dhdl-print-energy = no -sc-alpha = 0 -sc-power = 1 -sc-r-power = 6 -sc-sigma = 0.3 -sc-coul = no -separate-dhdl-file = yes -dhdl-derivatives = yes -dh_hist_size = 0 -dh_hist_spacing = 0.1 - -; Non-equilibrium MD stuff -acc-grps = -accelerate = -freezegrps = -freezedim = -cos-acceleration = 0 -deform = - -; simulated tempering variables -simulated-tempering = no -simulated-tempering-scaling = geometric -sim-temp-low = 300 -sim-temp-high = 300 - -; Electric fields -; Format is number of terms (int) and for all terms an amplitude (real) -; and a phase angle (real) -E-x = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -adress = no - -; User defined thingies -user1-grps = -user2-grps = -userint1 = 0 -userint2 = 0 -userint3 = 0 -userint4 = 0 -userreal1 = 0 -userreal2 = 0 -userreal3 = 0 -userreal4 = 0 diff --git a/testing/inputs/Gromacs/UnitTest/dihedral9/topol.tpr b/testing/inputs/Gromacs/UnitTest/dihedral9/topol.tpr deleted file mode 100644 index 28966fc25031a7c467aa3123ba0fcd6b77d95293..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4200 zcmdT`ZA_b06uyP>A%lqw?S>N@{N98BE#<52d)pU6@na3J@I#|+gc7nKAXJkP(N3d* z5u8r53HpPme~j5?VwRz@w$4PS8BZOhV&ct|z<13mK`2pJYD~xUz8r(W!(KeW#ItIx~BEyZRp~vsG}+rzgkkr5yA7 zl4BKij`{q5i=j_rZR&%aySsb3kbredt>0;M6syGxI>!6FWr|&%u>B1Ruh@Enk&}k@ zzJ_unv5f%R*s=^ldduGaVBk@*$R?!ugPnms!;R(k1^R>JqGr@-B@|sHsQEIb1`o0eyH3=FEG0f78*SzkZ>^%NqQQ&1S@*=g7ZMILR9I%86Ljac%PU z#_kAfieeuV_eKlB6RA3#T1f_LGR@Vm(0b*DMp+ZLOsYadP2~jE6vUmzSuyUrM;32% z=MOBfUe=hLKS;EF>9@HaKXrgL(flqL>1)mLJiRm$DVejdrp768EbGU8&b$R z&D%*iIGa2lt_d8^fw=`Sh`R+nvZCPNOBOxKy1N>j9vRYdnjI>$@_6+{jXzV%uAMiF}E_kEY zB(iv4x^#}zNn85^vUrzQIw~|-+V`%!qiaOEHnvK~WV5sdr=&|8lr`D+$f{@ajC{wO zMbbBc)bo1e_RC+$3je&U+x)V;Yq(P0eP&uVHXM~D^>4^+-LFco>oIxz;ZfJwg4S@P zdCL9d@l5SV`k<^I=+qwm?nI>MlRc3Qi=~mi#n0W&hmM7hHz zJpSX81?#Qyuv1+3otgfNPyLp*gn&G@4WB61WRhsR+V21A(%Zk)4ba7Wb2dwh5=V#& z_7!KIIgFj6jg5_K6JSNE7BY0=yOBH-bBK5+sBMTq^~u+4Hs_|`6nLCB*UzU8kcoGn zVXk<-@+A4mqMo^g?XkxCR+H7S!Nad|hTGJf)qFJ0tsrI83U3>^r|Z+)PTgR@S_)e*$V}(Cz>L