| Next changeset 1:c1fa72716efc (2019-12-01) |
|
Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit 4c75f8d26505d221d4144f4ae7d2fb7698fbe4ab" |
|
added:
alchemical_analysis/alchemical_analysis.xml alchemical_analysis/test-data/Free_energy_change_dF(t).txt alchemical_analysis/test-data/data.tar alchemical_run/gmx_fep.sh alchemical_run/test-data/Input_files.tar alchemical_run/test-data/Report.txt alchemical_run/test-data/TI_FEP_data_output.tar alchemical_run/test-data/morph.gro alchemical_run/test-data/morph.top |
| b |
| diff -r 000000000000 -r 5f136e371f44 alchemical_analysis/alchemical_analysis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_analysis/alchemical_analysis.xml Mon Nov 18 09:52:20 2019 -0500 |
| [ |
| @@ -0,0 +1,88 @@ +<tool id="alchemical_analysis" name="Alchemical Analysis" version="1.0.2"> + <description>Analysis of alchemical free energy calculations</description> + <requirements> + <requirement type="package" version="1.0.2">alchemical-analysis</requirement> + <requirement type="package" version="3.0.3">pymbar</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$datain' ./data.tar && + tar xf ./data.tar && + mkdir ./RESULTS/ && + #if $skiplambda == "": + alchemical_analysis -d data -o ./RESULTS -t '$temp' -s '$time' -c -q xvg -p '$prefix' -g -e -f 10 -w -u '$units' &>> '$output' + #else: + alchemical_analysis -d data -o ./RESULTS -t '$temp' -s '$time' -k '$skiplambda' -c -q xvg -p '$prefix' -g -e -f 10 -w -u '$units' &>> '$output' + #end if + ]]></command> + <inputs> + <param format="tar" name="datain" type="data" label="TI/FEP data output"/> + <param name="prefix" type="text" value="md" label="Prefix for datafile sets" help="This should be md if you used the alchemical simulator tool"/> + <param name="temp" type="integer" value="300" label="Temperature (K)"/> + <param name="time" type="integer" value="0" label="Equilibration time (ps)" help="Discard data prior to this specified time as 'equilibration' data." /> + <param name="units" type="select" label="Units to report energies" > + <option value="kcal">kcal</option> + <option value="kJ">kJ</option> + <option value="kBT">kT</option> + </param> + <param name="skiplambda" type="text" label="Indices of lambda states to skip" help="Give a string of lambda indices separated by '-' (e.g. 2-3) and they will be removed from the analysis. Default: will use all the windows."> + <validator type="regex" message="Only numeric values and '-' allowed">^[0-9-]*$</validator> + </param> + </inputs> + <outputs> + <data name="output" format="txt" label="output"> + </data> + <data name="results" format="txt" from_work_dir="./RESULTS/results.txt" label="Results"/> + <data name="change" format="txt" from_work_dir="./RESULTS/dF_t.txt" label="Free energy change dF(t)"/> + <data name="convergence" format="png" from_work_dir="./RESULTS/dF_t.png" label="Convergence Plot dF(t)"/> + <data name="overlap" format="png" from_work_dir="./RESULTS/O_MBAR.png" label="Overlap Matrix"/> + <data name="cfm" format="png" from_work_dir="./RESULTS/cfm.png" label="Curve Fitting Method (CFM) based consistency inspector"/> + <data name="df_state" format="png" from_work_dir="./RESULTS/dF_state_long.png" label="Free energy change breakdown"/> + <data name="ti_plot" format="png" from_work_dir="./RESULTS/dhdl_TI.png" label="Thermodynamic Integration plot"/> + </outputs> + <tests> + <test> + <param name="datain" value="data.tar" ftype="tar"/> + <param name="prefix" value="md"/> + <param name="temp" value="300"/> + <param name="time" value="0"/> + <param name="units" value="kcal"/> + <param name="lambda" value="no"/> + <output name="change" file="Free_energy_change_dF(t).txt" /> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + + +This tool can run analysis of alchemical free energy simulations. + +_____ + + +.. class:: infomark + +**Input** + + - TAR archive file of the GROMACS XVG files from free energy simulations. Note that simulations should be at least 100 ps in length. + +_____ + + +.. class:: infomark + +**Output** + + - Report and free energy outputs. + - Overlap matrix of free energy windows (as PNG). + - Convergence plot (as PNG). + - Curve Fitting Method (CFM) based consistency inspector (as PNG). + - Free energy change breakdown (as PNG). + - Thermodynamic Integration plot (as PNG). + + ]]></help> + <citations> + <citation type="doi">10.1007/s10822-015-9840-9</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 5f136e371f44 alchemical_analysis/test-data/Free_energy_change_dF(t).txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_analysis/test-data/Free_energy_change_dF(t).txt Mon Nov 18 09:52:20 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ + Time (ps) Forward (kcal/mol) Time (ps) Reverse (kcal/mol) + 50.0 6.818 +- 0.423 0.0 4.777 +- 0.174 + 100.0 5.623 +- 0.339 50.0 4.274 +- 0.187 + 150.0 5.071 +- 0.296 100.0 4.549 +- 0.199 + 200.0 5.131 +- 0.265 150.0 4.838 +- 0.216 + 250.0 4.806 +- 0.240 200.0 4.562 +- 0.232 + 300.0 5.004 +- 0.219 250.0 4.632 +- 0.259 + 350.0 4.771 +- 0.202 300.0 4.809 +- 0.286 + 400.0 4.852 +- 0.191 350.0 4.657 +- 0.304 + 450.0 4.918 +- 0.182 400.0 4.726 +- 0.344 + 500.0 4.777 +- 0.174 450.0 4.138 +- 0.463 |
| b |
| diff -r 000000000000 -r 5f136e371f44 alchemical_analysis/test-data/data.tar |
| b |
| Binary file alchemical_analysis/test-data/data.tar has changed |
| b |
| diff -r 000000000000 -r 5f136e371f44 alchemical_run/gmx_fep.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/gmx_fep.sh Mon Nov 18 09:52:20 2019 -0500 |
| b |
| @@ -0,0 +1,115 @@ +#!/bin/bash + +# _________ read inputs from the galaxy wrapper and define some variables ____________ + +lam=$1 +iter=$((lam+1)) + +mkdir MDP +mkdir data +mkdir traj + +FREE_ENERGY=`pwd` +MDP=$FREE_ENERGY/MDP + +set -e + +for i in `seq 0 $lam` + do + cp em_steep.mdp em_steep_$i.mdp + sed -i "s/%L%/$i/" em_steep_$i.mdp + cp nvt.mdp nvt_$i.mdp + sed -i "s/%L%/$i/" nvt_$i.mdp + cp npt.mdp npt_$i.mdp + sed -i "s/%L%/$i/" npt_$i.mdp + cp md.mdp md_$i.mdp + sed -i "s/%L%/$i/" md_$i.mdp + done +mv *.mdp $MDP + +for (( i=0; i<$iter; i++ )) +do + LAMBDA=$i + + # A new directory will be created for each value of lambda + + mkdir Lambda_$LAMBDA + cd Lambda_$LAMBDA + +# _______ ENERGY MINIMIZATION STEEP _______ + + echo "Starting minimization for lambda = $LAMBDA..." + + mkdir EM + cd EM + + # Iterative calls to grompp and mdrun to run the simulations + + gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/morph.gro -p $FREE_ENERGY/morph.top -o min$LAMBDA.tpr + + gmx mdrun -deffnm min$LAMBDA + + sleep 10 + + +# _______ NVT EQUILIBRATION _______ + + echo "Starting constant volume equilibration..." + + cd ../ + mkdir NVT + cd NVT + + gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/morph.top -o nvt$LAMBDA.tpr + + gmx mdrun -deffnm nvt$LAMBDA + + echo "Constant volume equilibration complete." + + sleep 10 + +# _______ NPT EQUILIBRATION _______ + + echo "Starting constant pressure equilibration..." + + cd ../ + mkdir NPT + cd NPT + + gmx grompp -f $MDP/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr + + gmx mdrun -deffnm npt$LAMBDA + + echo "Constant pressure equilibration complete." + + sleep 10 + +# ________ PRODUCTION MD ___________ + + echo "Starting production MD simulation..." + + cd ../ + mkdir Production_MD + cd Production_MD + + gmx grompp -f $MDP/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr + + gmx mdrun -deffnm md$LAMBDA + + echo "Production MD complete." + + # End + echo "Ending. Job completed for lambda = $LAMBDA" + + cd $FREE_ENERGY +done + +cp Lambda_*/Production_MD/*.xvg data/ +tar cf data.tar data/ + +cp Lambda_*/Production_MD/*.trr traj/ +tar cf traj.tar traj/ + +exit; + + |
| b |
| diff -r 000000000000 -r 5f136e371f44 alchemical_run/test-data/Input_files.tar |
| b |
| Binary file alchemical_run/test-data/Input_files.tar has changed |
| b |
| diff -r 000000000000 -r 5f136e371f44 alchemical_run/test-data/Report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/test-data/Report.txt Mon Nov 18 09:52:20 2019 -0500 |
| b |
| b'@@ -0,0 +1,1636 @@\n+Starting minimization for lambda = 0...\n+ :-) GROMACS - gmx grompp, 2019.1 (-:\n+\n+ GROMACS is written by:\n+ Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen\n+ Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd \n+ Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray \n+ Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang \n+ Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis\n+ Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n+ Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund \n+ Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall \n+ Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov \n+ Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen \n+ Christian Wennberg Maarten Wolf \n+ and the project leaders:\n+ Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n+\n+Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n+Copyright (c) 2001-2018, The GROMACS development team at\n+Uppsala University, Stockholm University and\n+the Royal Institute of Technology, Sweden.\n+check out http://www.gromacs.org for more information.\n+\n+GROMACS is free software; you can redistribute it and/or modify it\n+under the terms of the GNU Lesser General Public License\n+as published by the Free Software Foundation; either version 2.1\n+of the License, or (at your option) any later version.\n+\n+GROMACS: gmx grompp, version 2019.1\n+Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx\n+Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1\n+Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM\n+Command line:\n+ gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_0.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min0.tpr\n+\n+Setting the LD random seed to -127141127\n+Generated 45 of the 45 non-bonded parameter combinations\n+Generating 1-4 interactions: fudge = 0.5\n+Generated 45 of the 45 1-4 parameter combinations\n+Excluding 3 bonded neighbours molecule type \'Merged_Molecule\'\n+Excluding 3 bonded neighbours molecule type \'NA\'\n+Excluding 3 bonded neighbours molecule type \'CL\'\n+Excluding 3 bonded neighbours molecule type \'WAT\'\n+Removing all charge groups because cutoff-scheme=Verlet\n+Number of degrees of freedom in T-Coupling group rest is 12987.00\n+Estimate for the relative computational load of the PME mesh part: 0.21\n+\n+GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)\n+\n+Analysing residue names:\n+There are: 1 Other residues\n+There are: 10 Ion residues\n+There are: 2151 Water residues\n+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n+Calculating fourier grid dimensions for X Y Z\n+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111\n+This run will generate roughly 1 Mb of data\n+ :-) GROMACS - gmx mdrun, 2019.1 (-:\n+\n+ GROMACS is written by:\n+ Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen\n+ Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd \n+ Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray \n+ Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang \n+ Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis\n+ Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n+ Justin A. Lemkul Viveca'..b"errit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang \n+ Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis\n+ Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n+ Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund \n+ Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall \n+ Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov \n+ Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen \n+ Christian Wennberg Maarten Wolf \n+ and the project leaders:\n+ Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n+\n+Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n+Copyright (c) 2001-2018, The GROMACS development team at\n+Uppsala University, Stockholm University and\n+the Royal Institute of Technology, Sweden.\n+check out http://www.gromacs.org for more information.\n+\n+GROMACS is free software; you can redistribute it and/or modify it\n+under the terms of the GNU Lesser General Public License\n+as published by the Free Software Foundation; either version 2.1\n+of the License, or (at your option) any later version.\n+\n+GROMACS: gmx mdrun, version 2019.1\n+Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx\n+Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1\n+Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD\n+Command line:\n+ gmx mdrun -deffnm md2\n+\n+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).\n+The current CPU can measure timings more accurately than the code in\n+gmx mdrun was configured to use. This might affect your simulation\n+speed as accurate timings are needed for load-balancing.\n+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.\n+Reading file md2.tpr, VERSION 2019.1 (single precision)\n+Changing nstlist from 10 to 50, rlist from 0.8 to 0.86\n+\n+\n+Using 1 MPI thread\n+Using 4 OpenMP threads \n+\n+starting mdrun 'BioSimSpace System'\n+2000 steps, 2.0 ps.\n+\n+step 2: One or more water molecules can not be settled.\n+Check for bad contacts and/or reduce the timestep if appropriate.\n+Wrote pdb files with previous and current coordinates\n+\n+WARNING: Listed nonbonded interaction between particles 6 and 15\n+at distance 47.750 which is larger than the table limit 1.860 nm.\n+\n+This is likely either a 1,4 interaction, or a listed interaction inside\n+a smaller molecule you are decoupling during a free energy calculation.\n+Since interactions at distances beyond the table cannot be computed,\n+they are skipped until they are inside the table limit again. You will\n+only see this message once, even if it occurs for several interactions.\n+\n+IMPORTANT: This should not happen in a stable simulation, so there is\n+probably something wrong with your system. Only change the table-extension\n+distance in the mdp file if you are really sure that is the reason.\n+\n+\n+\n+WARNING: Listed nonbonded interaction between particles 2 and 15\n+at distance 47.627 which is larger than the table limit 1.860 nm.\n+\n+This is likely either a 1,4 interaction, or a listed interaction inside\n+a smaller molecule you are decoupling during a free energy calculation.\n+Since interactions at distances beyond the table cannot be computed,\n+they are skipped until they are inside the table limit again. You will\n+only see this message once, even if it occurs for several interactions.\n+\n+IMPORTANT: This should not happen in a stable simulation, so there is\n+probably something wrong with your system. Only change the table-extension\n+distance in the mdp file if you are really sure that is the reason.\n+\n+\n+/scratch2/tsenapathi/Projects/BRIDGE/galaxy-tools-compchem/tools/free_energy/alchemical_run/gmx_fep.sh: line 104: 13890 Segmentation fault gmx mdrun -deffnm md$LAMBDA\n+Production MD complete.\n+Ending. Job completed for lambda = 2\n" |
| b |
| diff -r 000000000000 -r 5f136e371f44 alchemical_run/test-data/TI_FEP_data_output.tar |
| b |
| Binary file alchemical_run/test-data/TI_FEP_data_output.tar has changed |
| b |
| diff -r 000000000000 -r 5f136e371f44 alchemical_run/test-data/morph.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/test-data/morph.gro Mon Nov 18 09:52:20 2019 -0500 |
| b |
| b'@@ -0,0 +1,6484 @@\n+GROningen MAchine for Chemical Simulation\n+ 6481\n+ 1LIG C 1 1.955 1.939 2.023\n+ 1LIG C1 2 1.997 1.913 1.895\n+ 1LIG C2 3 2.091 1.992 1.835\n+ 1LIG C3 4 2.141 2.098 1.902\n+ 1LIG C4 5 2.099 2.126 2.030\n+ 1LIG C5 6 2.007 2.044 2.092\n+ 1LIG H 7 1.881 1.875 2.069\n+ 1LIG H1 8 1.955 1.829 1.841\n+ 1LIG H2 9 2.124 1.970 1.734\n+ 1LIG H3 10 2.215 2.162 1.854\n+ 1LIG H4 11 2.140 2.211 2.084\n+ 1LIG H5 12 1.975 2.064 2.193\n+ 1LIG H 13 1.838 1.789 2.010\n+ 1LIG H1 14 1.921 1.817 2.156\n+ 1LIG H2 15 1.786 1.927 2.095\n+ 1LIG H7 16 2.022 2.150 2.248\n+ 1LIG H8 17 1.868 2.096 2.200\n+ 1LIG H9 18 1.999 1.983 2.266\n+ 2NA NA 19 0.461 1.266 1.727\n+ 3NA NA 20 0.225 2.137 2.858\n+ 4NA NA 21 1.400 3.831 0.426\n+ 5NA NA 22 0.614 3.846 1.979\n+ 6NA NA 23 2.064 2.147 3.360\n+ 7CL CL 24 1.730 0.934 1.517\n+ 8CL CL 25 0.594 0.745 2.514\n+ 9CL CL 26 0.473 4.224 3.915\n+ 10CL CL 27 2.721 1.374 0.016\n+ 11CL CL 28 2.244 0.700 2.342\n+ 12WAT O 29 0.230 0.628 0.113\n+ 12WAT H1 30 0.137 0.626 0.150\n+ 12WAT H2 31 0.231 0.589 0.021\n+ 13WAT O 32 0.225 0.275 0.996\n+ 13WAT H1 33 0.260 0.258 1.088\n+ 13WAT H2 34 0.137 0.230 0.984\n+ 14WAT O 35 0.019 0.368 0.647\n+ 14WAT H1 36 -0.063 0.411 0.686\n+ 14WAT H2 37 -0.009 0.295 0.584\n+ 15WAT O 38 0.569 1.275 1.165\n+ 15WAT H1 39 0.476 1.268 1.128\n+ 15WAT H2 40 0.580 1.364 1.209\n+ 16WAT O 41 1.555 1.511 0.703\n+ 16WAT H1 42 1.498 1.495 0.784\n+ 16WAT H2 43 1.496 1.521 0.623\n+ 17WAT O 44 1.135 0.703 0.717\n+ 17WAT H1 45 1.192 0.781 0.692\n+ 17WAT H2 46 1.075 0.729 0.793\n+ 18WAT O 47 1.755 0.607 0.231\n+ 18WAT H1 48 1.743 0.594 0.132\n+ 18WAT H2 49 1.725 0.526 0.280\n+ 19WAT O 50 0.768 1.144 1.023\n+ 19WAT H1 51 0.690 1.161 1.083\n+ 19WAT H2 52 0.802 1.231 0.987\n+ 20WAT O 53 0.850 0.798 1.823\n+ 20WAT H1 54 0.846 0.874 1.888\n+ 20WAT H2 55 0.872 0.834 1.732\n+ 21WAT O 56 0.685 1.012 0.665\n+ 21WAT H1 57 0.754 0.996 0.735\n+ 21WAT H2 58 0.612 1.069 0.703\n+ 22WAT O 59 0.686 1.161 1.803\n+ 22WAT H1 60 0.746 1.240 1.817\n+ 22WAT H2 61 0.600 1.192 1.762\n+ 23WAT O 62 0.335 1.435 1.061\n+ 23WAT H1 63 0.257 1.404 1.008\n+ 23WAT H2 64 0.393 1.493 1.004\n+ 24WAT O 65 1.460 1.505 1.339\n+ 24WAT H1 66 1.484 1.599 1.365\n+ 24WAT H2 67 1.444 1.451 1.421\n+ 25WAT O 68 0.438 0.392 1.499\n+ 25WAT H1 69 0.520 0.336 1.508\n+ 25WAT H2 70 0.357 0.334 1.503\n+ 26WAT O 71 1.603 0.447 0.737\n+ 26WAT H1 72 1.529 0.493 0.687\n+ 26WAT H2 73 1.654 0.515 0.790\n+ 27WAT O 74 0.231 1.713 0.483\n+ 27WAT H1 75 0.265 1.790 0.537\n+ 27WAT H2 76 0.275 1.713 0.393\n+ 28WAT O 77 1.127 1.341 1.690\n+ 28WAT H1 78 1.174 1.341 1.778\n+ 28WAT H2 79 1.079 1.254 1.679\n+ 29WAT O 80 0.230 1.434 0.538\n+ 29WAT H1 81 0.204 1.530 0.538\n+ 29WAT H2 82 0.159 1.380 0.583\n+ 30WAT O 83 0.240 1.091 0.886\n+ 30WAT H1 84 0.254 1.007 0.938\n+ 30WAT H2 85 0.185 1.155 0.941\n+ 31WAT O 8'..b'07 1.895\n+ 2134WAT H1 6396 3.707 2.179 1.866\n+ 2134WAT H2 6397 3.830 2.284 1.839\n+ 2135WAT O 6398 3.796 2.028 2.180\n+ 2135WAT H1 6399 3.779 2.111 2.126\n+ 2135WAT H2 6400 3.886 1.991 2.158\n+ 2136WAT O 6401 3.803 3.102 2.515\n+ 2136WAT H1 6402 3.802 3.055 2.603\n+ 2136WAT H2 6403 3.885 3.074 2.464\n+ 2137WAT O 6404 3.763 2.939 2.162\n+ 2137WAT H1 6405 3.862 2.928 2.153\n+ 2137WAT H2 6406 3.723 2.853 2.194\n+ 2138WAT O 6407 3.954 2.490 3.837\n+ 2138WAT H1 6408 3.861 2.488 3.874\n+ 2138WAT H2 6409 3.955 2.451 3.745\n+ 2139WAT O 6410 3.751 3.458 3.841\n+ 2139WAT H1 6411 3.732 3.362 3.862\n+ 2139WAT H2 6412 3.718 3.516 3.916\n+ 2140WAT O 6413 4.021 1.897 3.895\n+ 2140WAT H1 6414 4.070 1.981 3.874\n+ 2140WAT H2 6415 4.083 1.832 3.940\n+ 2141WAT O 6416 4.251 2.118 4.052\n+ 2141WAT H1 6417 4.278 2.059 3.977\n+ 2141WAT H2 6418 4.251 2.213 4.021\n+ 2142WAT O 6419 3.732 3.188 3.924\n+ 2142WAT H1 6420 3.639 3.209 3.893\n+ 2142WAT H2 6421 3.742 3.089 3.937\n+ 2143WAT O 6422 3.799 2.207 3.757\n+ 2143WAT H1 6423 3.707 2.179 3.728\n+ 2143WAT H2 6424 3.830 2.284 3.701\n+ 2144WAT O 6425 3.763 2.939 4.024\n+ 2144WAT H1 6426 3.862 2.928 4.015\n+ 2144WAT H2 6427 3.723 2.853 4.056\n+ 2145WAT O 6428 3.949 3.999 0.996\n+ 2145WAT H1 6429 3.984 3.982 1.088\n+ 2145WAT H2 6430 3.861 3.954 0.984\n+ 2146WAT O 6431 3.743 4.092 0.647\n+ 2146WAT H1 6432 3.661 4.135 0.686\n+ 2146WAT H2 6433 3.715 4.019 0.584\n+ 2147WAT O 6434 3.926 4.009 1.498\n+ 2147WAT H1 6435 3.846 4.069 1.485\n+ 2147WAT H2 6436 3.916 3.960 1.584\n+ 2148WAT O 6437 4.021 3.759 0.171\n+ 2148WAT H1 6438 4.070 3.843 0.150\n+ 2148WAT H2 6439 4.083 3.694 0.216\n+ 2149WAT O 6440 4.031 3.937 1.231\n+ 2149WAT H1 6441 4.008 3.974 1.321\n+ 2149WAT H2 6442 4.001 3.842 1.225\n+ 2150WAT O 6443 4.031 3.787 0.618\n+ 2150WAT H1 6444 4.020 3.881 0.651\n+ 2150WAT H2 6445 4.026 3.724 0.695\n+ 2151WAT O 6446 3.799 4.069 0.033\n+ 2151WAT H1 6447 3.707 4.041 0.004\n+ 2151WAT H2 6448 3.830 4.146 -0.023\n+ 2152WAT O 6449 3.796 3.890 0.318\n+ 2152WAT H1 6450 3.779 3.973 0.264\n+ 2152WAT H2 6451 3.886 3.853 0.296\n+ 2153WAT O 6452 3.949 3.999 2.858\n+ 2153WAT H1 6453 3.984 3.982 2.950\n+ 2153WAT H2 6454 3.861 3.954 2.846\n+ 2154WAT O 6455 3.743 4.092 2.509\n+ 2154WAT H1 6456 3.661 4.135 2.548\n+ 2154WAT H2 6457 3.715 4.019 2.446\n+ 2155WAT O 6458 3.926 4.009 3.360\n+ 2155WAT H1 6459 3.846 4.069 3.347\n+ 2155WAT H2 6460 3.916 3.960 3.446\n+ 2156WAT O 6461 4.021 3.759 2.033\n+ 2156WAT H1 6462 4.070 3.843 2.012\n+ 2156WAT H2 6463 4.083 3.694 2.078\n+ 2157WAT O 6464 4.031 3.937 3.093\n+ 2157WAT H1 6465 4.008 3.974 3.183\n+ 2157WAT H2 6466 4.001 3.842 3.087\n+ 2158WAT O 6467 4.031 3.787 2.480\n+ 2158WAT H1 6468 4.020 3.881 2.513\n+ 2158WAT H2 6469 4.026 3.724 2.557\n+ 2159WAT O 6470 3.799 4.069 1.895\n+ 2159WAT H1 6471 3.707 4.041 1.866\n+ 2159WAT H2 6472 3.830 4.146 1.839\n+ 2160WAT O 6473 3.796 3.890 2.180\n+ 2160WAT H1 6474 3.779 3.973 2.126\n+ 2160WAT H2 6475 3.886 3.853 2.158\n+ 2161WAT O 6476 4.021 3.759 3.895\n+ 2161WAT H1 6477 4.070 3.843 3.874\n+ 2161WAT H2 6478 4.083 3.694 3.940\n+ 2162WAT O 6479 3.799 4.069 3.757\n+ 2162WAT H1 6480 3.707 4.041 3.728\n+ 2162WAT H2 6481 3.830 4.146 3.701\n+ 4.00000 4.00000 4.00000\n' |
| b |
| diff -r 000000000000 -r 5f136e371f44 alchemical_run/test-data/morph.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/test-data/morph.top Mon Nov 18 09:52:20 2019 -0500 |
| [ |
| b'@@ -0,0 +1,232 @@\n+; Gromacs Topology File written by Sire\n+; File written 05/01/19 13:21:14\n+[ defaults ]\n+; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ\n+ 1 2 yes 0.5 0.833333\n+\n+[ atomtypes ]\n+; name at.num mass charge ptype sigma epsilon\n+ Cl- 17 35.453000 0.000000 A 0.447766 0.148913\n+ HW 1 1.007940 0.000000 A 0.000000 0.000000\n+ Na+ 11 22.989770 0.000000 A 0.243928 0.365846\n+ OW 8 15.999400 0.000000 A 0.315075 0.635968\n+ c3 6 12.010700 0.000000 A 0.339771 0.451035\n+ ca 6 12.010700 0.000000 A 0.331521 0.413379\n+ ha 1 1.007940 0.000000 A 0.262548 0.067362\n+ hc 1 1.007940 0.000000 A 0.260018 0.087027\n+ hc_du 0 0.000000 0.000000 A 0.000000 0.000000\n+\n+[ moleculetype ]\n+; name nrexcl\n+CL 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass\n+ 1 Cl- 1 CL CL 1 -1.000000 35.450000\n+\n+\n+[ moleculetype ]\n+; name nrexcl\n+Merged_Molecule 3\n+\n+[ atoms ]\n+; nr type0 resnr residue atom cgnr charge0 mass0 type1 charge1 mass1\n+ 1 ca 1 LIG C 1 -0.130000 12.010000 ca -0.075744 12.010000\n+ 2 ca 1 LIG C1 2 -0.130000 12.010000 ca -0.129444 12.010000\n+ 3 ca 1 LIG C2 3 -0.130000 12.010000 ca -0.131444 12.010000\n+ 4 ca 1 LIG C3 4 -0.130000 12.010000 ca -0.131444 12.010000\n+ 5 ca 1 LIG C4 5 -0.130000 12.010000 ca -0.129444 12.010000\n+ 6 ca 1 LIG C5 6 -0.130000 12.010000 ca -0.075744 12.010000\n+ 7 ha 1 LIG H 7 0.130000 1.008000 c3 -0.053744 12.010000\n+ 8 ha 1 LIG H1 8 0.130000 1.008000 ha 0.129056 1.008000\n+ 9 ha 1 LIG H2 9 0.130000 1.008000 ha 0.130056 1.008000\n+ 10 ha 1 LIG H3 10 0.130000 1.008000 ha 0.130056 1.008000\n+ 11 ha 1 LIG H4 11 0.130000 1.008000 ha 0.129056 1.008000\n+ 12 ha 1 LIG H5 12 0.130000 1.008000 c3 -0.053744 12.010000\n+ 13 hc_du 1 LIG H 13 0.000000 1.008000 hc 0.043756 1.008000\n+ 14 hc_du 1 LIG H1 14 0.000000 1.008000 hc 0.043756 1.008000\n+ 15 hc_du 1 LIG H2 15 0.000000 1.008000 hc 0.043756 1.008000\n+ 16 hc_du 1 LIG H7 16 0.000000 1.008000 hc 0.043756 1.008000\n+ 17 hc_du 1 LIG H8 17 0.000000 1.008000 hc 0.043756 1.008000\n+ 18 hc_du 1 LIG H9 18 0.000000 1.008000 hc 0.043756 1.008000\n+\n+[ bonds ]\n+; ai aj funct parameters\n+ 1 2 1 0.1398 316812 0.1398 316812\n+ 1 6 1 0.1398 316812 0.1398 316812\n+ 1 7 1 0.1086 331122 0.1516 209451\n+ 2 3 1 0.1398 316812 0.1398 316812\n+ 2 8 1 0.1086 331122 0.1086 331122\n+ 3 4 1 0.1398 316812 0.1398 316812\n+ 3 9 1 0.1086 331122 0.1086 331122\n+ 4 5 1 0.1398 316812 0.1398 316812\n+ 4 10 1 0.1086 331122 0.1086 331122\n+ 5 6 1 0.1398 316812 0.1398 316812\n+ 5 11 1 0.1086 331122 0.1086 331122\n+ 6 12 1 0.1086 331122 0.1516 209451\n+ 7 13 1 0.1097 314553 0.1097 314553\n+ 7 14 1 0.1097 314553 0.1097 314553\n+ 7 15 '..b'2 107.58 326.352\n+ 13 7 15 1 107.58 326.352 107.58 326.352\n+ 14 7 15 1 107.58 326.352 107.58 326.352\n+ 16 12 17 1 107.58 326.352 107.58 326.352\n+ 16 12 18 1 107.58 326.352 107.58 326.352\n+ 17 12 18 1 107.58 326.352 107.58 326.352\n+\n+[ dihedrals ]\n+; ai aj ak al funct parameters\n+ 1 2 3 4 1 180 15.167 2 180 15.167 2\n+ 1 2 3 9 1 180 15.167 2 180 15.167 2\n+ 1 3 2 8 4 180 4.6024 2 180 4.6024 2\n+ 1 5 6 12 4 180 4.6024 2 0 0 2\n+ 1 6 5 4 1 180 15.167 2 180 15.167 2\n+ 1 6 5 11 1 180 15.167 2 180 15.167 2\n+ 1 6 12 16 1 0 0 0 0 0 0\n+ 1 6 12 17 1 0 0 0 0 0 0\n+ 1 6 12 18 1 0 0 0 0 0 0\n+ 2 1 6 5 1 180 15.167 2 180 15.167 2\n+ 2 1 6 12 1 180 15.167 2 180 15.167 2\n+ 2 1 7 13 1 0 0 0 0 0 0\n+ 2 1 7 14 1 0 0 0 0 0 0\n+ 2 1 7 15 1 0 0 0 0 0 0\n+ 2 3 4 5 1 180 15.167 2 180 15.167 2\n+ 2 3 4 10 1 180 15.167 2 180 15.167 2\n+ 2 4 3 9 4 180 4.6024 2 180 4.6024 2\n+ 2 6 1 7 4 180 4.6024 2 180 4.6024 2\n+ 3 2 1 6 1 180 15.167 2 180 15.167 2\n+ 3 2 1 7 1 180 15.167 2 180 15.167 2\n+ 3 4 5 6 1 180 15.167 2 180 15.167 2\n+ 3 4 5 11 1 180 15.167 2 180 15.167 2\n+ 3 5 4 10 4 180 4.6024 2 180 4.6024 2\n+ 4 3 2 8 1 180 15.167 2 180 15.167 2\n+ 4 5 6 12 1 180 15.167 2 180 15.167 2\n+ 4 6 5 11 4 180 4.6024 2 180 4.6024 2\n+ 5 4 3 9 1 180 15.167 2 180 15.167 2\n+ 5 6 1 7 1 180 15.167 2 180 15.167 2\n+ 5 6 1 12 4 0 0 2 180 4.6024 2\n+ 5 6 12 16 1 0 0 0 0 0 0\n+ 5 6 12 17 1 0 0 0 0 0 0\n+ 5 6 12 18 1 0 0 0 0 0 0\n+ 6 1 2 8 1 180 15.167 2 180 15.167 2\n+ 6 1 7 13 1 0 0 0 0 0 0\n+ 6 1 7 14 1 0 0 0 0 0 0\n+ 6 1 7 15 1 0 0 0 0 0 0\n+ 6 5 4 10 1 180 15.167 2 180 15.167 2\n+ 7 1 2 8 1 180 15.167 2 180 15.167 2\n+ 7 1 6 12 1 180 15.167 2 180 15.167 2\n+ 8 2 3 9 1 180 15.167 2 180 15.167 2\n+ 9 3 4 10 1 180 15.167 2 180 15.167 2\n+ 10 4 5 11 1 180 15.167 2 180 15.167 2\n+ 11 5 6 12 1 180 15.167 2 180 15.167 2\n+\n+\n+[ moleculetype ]\n+; name nrexcl\n+NA 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass\n+ 1 Na+ 1 NA NA 1 1.000000 22.990000\n+\n+\n+[ moleculetype ]\n+; name nrexcl\n+WAT 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass\n+ 1 OW 1 WAT O 1 -0.834000 16.000000\n+ 2 HW 1 WAT H1 2 0.417000 1.008000\n+ 3 HW 1 WAT H2 3 0.417000 1.008000\n+\n+#ifdef FLEXIBLE\n+#else\n+\n+[ settles ]\n+; OW funct doh dhh\n+1 1 0.09572 0.15136\n+\n+[ exclusions ]\n+1 2 3\n+2 1 3\n+3 1 2\n+\n+#endif\n+\n+[ system ]\n+BioSimSpace System\n+\n+[ molecules ]\n+;molecule name nr.\n+Merged_Molecule 1\n+ NA 5\n+ CL 5\n+ WAT 2151\n+\n' |