| Next changeset 1:93e39b0321c7 (2018-10-04) |
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Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618 |
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added:
macros.xml npt.xml test-data/1AKI.pdb test-data/em.edr test-data/em.gro test-data/em.tpr test-data/em.trr test-data/ions.mdp test-data/ions.tpr test-data/md.mdp test-data/md_0_1.cpt test-data/md_0_1.edr test-data/md_0_1.gro test-data/md_0_1.pdb test-data/md_0_1.tpr test-data/md_0_1.trr test-data/md_0_1.xtc test-data/minim.mdp test-data/newbox.gro test-data/npt.cpt test-data/npt.edr test-data/npt.gro test-data/npt.mdp test-data/npt.pdb test-data/npt.tpr test-data/npt.trr test-data/npt.xtc test-data/nvt.cpt test-data/nvt.edr test-data/nvt.gro test-data/nvt.mdp test-data/nvt.pdb test-data/nvt.tpr test-data/nvt.trr test-data/nvt.xtc test-data/posres.itp test-data/processed.gro test-data/solv.gro test-data/solv_ions.gro test-data/topol.top test-data/topol_solv.top |
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| diff -r 000000000000 -r 69ff679edefd macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Oct 04 17:38:27 2018 -0400 |
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| @@ -0,0 +1,93 @@ +<macros> + <token name="@VERSION@">2018.2</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">gromacs</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1016/j.softx.2015.06.001</citation> + </citations> + </xml> + + + <xml name="md_inputs"> + <conditional name="mdp"> + <param name="mdpfile" type="select" label="Parameter input"> + <option value="custom">Upload own MDP file</option> + <option value="default">Use default (partially customisable) setting</option> + </param> + <when value="custom"> + <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/> + </when> + <when value="default"> + <param argument="integrator" type="select" label="Choice of integrator."> + <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> + <option value="sd">Stochastic dynamics integrator</option> + <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> + </param> + <param argument="constraints" type="select" label="Bond constraints (constraints)."> + <option value="none">No constraints except for those defined explicitly in the topology (none).</option> + <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> + <option value="all-bonds">All bonds (all-bonds).</option> + <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> + <option value="all-angles">All bonds and angles (all-angles).</option> + </param> + <param argument="cutoffscheme" type="select" label="Neighbor searching."> + <option value="Verlet">Generate a pair list with buffering.</option> + <option value="group">Generate a pair list for groups of atoms.</option> + </param> + <param argument="coulombtype" type="select" label="Electrostatics."> + <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> + <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> + <option value="Reaction-Field-zero">Reaction field electrostatics.</option> + </param> + + <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" /> + <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> + <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." /> + <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> + <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/> + <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> + <param argument="md_steps" type="integer" label="Number of steps for the NPT equilibration" value="0" min="0" max="1000000" help="NPT steps" /> + + </when> + + </conditional> + + <param argument="traj" type="select" label="Trajectory output."> + <option value='none'>Return no trajectory output</option> + <option value='xtc'>Return .xtc file (reduced precision)</option> + <option value='trr'>Return .trr file (full precision)</option> + <option value='both'>Return both .xtc and .trr files</option> + </param> + + <param argument="str" type="select" label="Structure output."> + <option value='none'>Return no trajectory output</option> + <option value='gro'>Return .gro file</option> + <option value='pdb'>Return .pdb file</option> + <option value='both'>Return both .gro and .pdb files</option> + </param> + + <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> + + + </xml> + + + <xml name="test_params"> + <param name="mdpfile" value="default" /> + <param name="step_length" value="0.002"/> + <param name="md_steps" value="500"/> + <param name="write_freq" value="50"/> + <param name="temperature" value="300"/> + <param name="integrator" value="md" /> + <param name="constraints" value="all-bonds"/> + <param name="cutoffscheme" value="Verlet" /> + <param name="coulombtype" value="PME" /> + <param name="rlist" value="1.0" /> + <param name="rcoulomb" value="1.0" /> + <param name="rvdw" value="1.0" /> + </xml> +</macros> |
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| diff -r 000000000000 -r 69ff679edefd npt.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/npt.xml Thu Oct 04 17:38:27 2018 -0400 |
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| b'@@ -0,0 +1,180 @@\n+<tool id="gmx_npt" name="GROMACS NPT equilibration" version="@VERSION@">\n+ <description>- constant-temperature and -pressure equilibration of a system</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements" />\n+\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $mdp.mdpfile == "custom":\n+ ln -s \'$mdp.mdp_input\' ./npt.mdp &&\n+ #end if\n+ #if $mdp.mdpfile == "default":\n+ ln -s \'$npt\' ./npt.mdp &&\n+ #end if\n+\n+ ln -s \'$gro_input\' ./nvt.gro &&\n+ ln -s \'$cpt_input\' ./nvt.cpt &&\n+ ln -s \'$top_input\' ./top_input.top &&\n+ ln -s \'$itp_input\' ./posres.itp &&\n+\n+ gmx grompp -f ./npt.mdp -c ./nvt.gro -r ./nvt.gro -t ./nvt.cpt -p ./top_input.top -o npt.tpr &>> verbose.txt &&\n+ gmx mdrun -deffnm npt &>> verbose.txt\n+\n+ #if $str == \'pdb\' or $str == \'both\'\n+ && gmx editconf -f npt.gro -o npt.pdb &>> verbose.txt\n+ #end if\n+\n+ ]]></command>\n+ <configfiles>\n+ <!-- .mdp file for the gromacs simulation -->\n+ <configfile name="npt">\n+ #if $mdp.mdpfile == \'default\':\n+ title = NPT equilibration \n+ define = -DPOSRES ; position restrain the protein\n+ ; Run parameters\n+ integrator = $mdp.integrator ; leap-frog integrator\n+ nsteps = $mdp.md_steps ; 2 * 50000 = 100 ps\n+ dt = $mdp.step_length ; 2 fs\n+ ; Output control\n+ nstxout = $mdp.write_freq ; save coordinates every 1.0 ps\n+ nstvout = $mdp.write_freq ; save velocities every 1.0 ps\n+ nstenergy = $mdp.write_freq ; save energies every 1.0 ps\n+ nstlog = $mdp.write_freq ; update log file every 1.0 ps\n+ nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps\n+\n+ ; Bond parameters\n+ continuation = yes ; Restarting after NVT \n+ constraint_algorithm = lincs ; holonomic constraints \n+ constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained\n+ lincs_iter = 1 ; accuracy of LINCS\n+ lincs_order = 4 ; also related to accuracy\n+ ; Neighborsearching\n+ cutoff-scheme = $mdp.cutoffscheme\n+ ns_type = grid ; search neighboring grid cells\n+ nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme\n+ rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off\n+ rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.\n+ rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off\n+ ; Electrostatics\n+ coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME\n+ pme_order = 4 ; cubic interpolation\n+ fourierspacing = 0.16 ; grid spacing for FFT\n+ ; Temperature coupling is on\n+ tcoupl = V-rescale ; modified Berendsen thermostat\n+ tc-grps = Protein Non-Protein ; two coupling groups - more accurate\n+ tau_t = 0.1 0.1 ; time constant, in ps\n+ ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K\n+ ; Pressure coupling is on\n+ pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT\n+ pcoupltype = isotropic '..b'utput1" format="gro" from_work_dir="npt.gro">\n+ <filter>str == \'gro\' or str == \'both\'</filter>\n+ </data>\n+ <data name="output5" format="pdb" from_work_dir="npt.pdb">\n+ <filter>str == \'pdb\' or str == \'both\'</filter>\n+ </data>\n+ <data name="output2" format="cpt" from_work_dir="npt.cpt"/>\n+ <data name="output3" format="trr" from_work_dir="npt.trr">\n+ <filter>traj == \'trr\' or traj == \'both\'</filter>\n+ </data>\n+ <data name="output4" format="xtc" from_work_dir="npt.xtc">\n+ <filter>traj == \'xtc\' or traj == \'both\'</filter>\n+ </data>\n+ <data name="report" format="txt" from_work_dir="verbose.txt">\n+ <filter>capture_log</filter>\n+ </data>\n+ </outputs>\n+ \n+ <tests>\n+ <test>\n+ <param name="gro_input" value="nvt.gro" />\n+ <param name="top_input" value="topol_solv.top" />\n+ <param name="cpt_input" value="nvt.cpt" />\n+ <param name="itp_input" value="posres.itp" />\n+ <param name="traj" value="xtc"/>\n+ <param name="str" value="both"/>\n+ \n+ <expand macro="test_params"/>\n+ \n+ <output name="output1" file="npt.gro" ftype="gro" compare="sim_size"/>\n+ <output name="output2" file="npt.cpt" ftype="cpt" compare="sim_size"/>\n+ <output name="output4" file="npt.xtc" ftype="xtc" compare="sim_size"/>\n+ <output name="output5" file="npt.pdb" ftype="pdb" compare="sim_size"/>\n+ </test>\n+ \n+ <test>\n+ <param name="gro_input" value="nvt.gro" />\n+ <param name="top_input" value="topol_solv.top" />\n+ <param name="cpt_input" value="nvt.cpt" />\n+ <param name="itp_input" value="posres.itp" />\n+ <param name="traj" value="xtc"/>\n+ <param name="str" value="pdb"/>\n+ \n+ <expand macro="test_params"/>\n+ \n+ <output name="output2" file="npt.cpt" ftype="cpt" compare="sim_size"/>\n+ <output name="output4" file="npt.xtc" ftype="xtc" compare="sim_size"/>\n+ <output name="output5" file="npt.pdb" ftype="pdb" compare="sim_size"/>\n+ </test>\n+\n+ <test>\n+ <param name="gro_input" value="nvt.gro" />\n+ <param name="top_input" value="topol_solv.top" />\n+ <param name="cpt_input" value="nvt.cpt" />\n+ <param name="itp_input" value="posres.itp" />\n+ <param name="str" value="none"/>\n+ <param name="traj" value="trr"/>\n+ \n+ <expand macro="test_params"/>\n+ \n+ <output name="output2" file="npt.cpt" ftype="cpt" compare="sim_size"/>\n+ <output name="output3" file="npt.trr" ftype="trr" compare="sim_size"/>\n+ </test>\n+\n+ <test>\n+ <param name="gro_input" value="nvt.gro" />\n+ <param name="top_input" value="topol_solv.top" />\n+ <param name="cpt_input" value="nvt.cpt" />\n+ <param name="itp_input" value="posres.itp" />\n+ <param name="mdpfile" value="custom" />\n+ <param name="mdp_input" value="npt.mdp" />\n+ <param name="traj" value="none"/>\n+ <param name="str" value="gro"/>\n+ <output name="output1" file="npt.gro" ftype="gro" compare="sim_size"/>\n+ <output name="output2" file="npt.cpt" ftype="cpt" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+Upload GRO, TOP and ITP (position restraint) files for equilibration under an NPT ensemble, as well as the checkpoint (CPT) file from the NVT equilibration. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/online/mdp_opt.html for more information on the options.\n+\n+ ]]></help>\n+\n+ <expand macro="citations" />\n+ \n+ </tool>\n' |
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| diff -r 000000000000 -r 69ff679edefd test-data/1AKI.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1AKI.pdb Thu Oct 04 17:38:27 2018 -0400 |
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| b'@@ -0,0 +1,1436 @@\n+HEADER HYDROLASE 19-MAY-97 1AKI \n+TITLE THE STRUCTURE OF THE ORTHORHOMBIC FORM OF HEN EGG-WHITE \n+TITLE 2 LYSOZYME AT 1.5 ANGSTROMS RESOLUTION \n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: LYSOZYME; \n+COMPND 3 CHAIN: A; \n+COMPND 4 EC: 3.2.1.17 \n+SOURCE MOL_ID: 1; \n+SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; \n+SOURCE 3 ORGANISM_COMMON: CHICKEN; \n+SOURCE 4 ORGANISM_TAXID: 9031; \n+SOURCE 5 CELL: EGG \n+KEYWDS HYDROLASE, GLYCOSIDASE \n+EXPDTA X-RAY DIFFRACTION \n+AUTHOR D.CARTER,J.HE,J.R.RUBLE,B.WRIGHT \n+REVDAT 2 24-FEB-09 1AKI 1 VERSN \n+REVDAT 1 19-NOV-97 1AKI 0 \n+JRNL AUTH P.J.ARTYMIUK,C.C.F.BLAKE,D.W.RICE,K.S.WILSON \n+JRNL TITL THE STRUCTURES OF THE MONOCLINIC AND ORTHORHOMBIC \n+JRNL TITL 2 FORMS OF HEN EGG-WHITE LYSOZYME AT 6 ANGSTROMS \n+JRNL TITL 3 RESOLUTION \n+JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 38 778 1982 \n+JRNL REFN ISSN 0108-7681 \n+REMARK 1 \n+REMARK 2 \n+REMARK 2 RESOLUTION. 1.50 ANGSTROMS. \n+REMARK 3 \n+REMARK 3 REFINEMENT. \n+REMARK 3 PROGRAM : GPRLSA, X-PLOR \n+REMARK 3 AUTHORS : FUREY \n+REMARK 3 \n+REMARK 3 DATA USED IN REFINEMENT. \n+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 \n+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 \n+REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 \n+REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 \n+REMARK 3 NUMBER OF REFLECTIONS : 16327 \n+REMARK 3 \n+REMARK 3 FIT TO DATA USED IN REFINEMENT. \n+REMARK 3 CROSS-VALIDATION METHOD : NULL \n+REMARK 3 FREE R VALUE TEST SET SELECTION : NULL \n+REMARK 3 R VALUE (WORKING + TEST SET) : NULL \n+REMARK 3 R VALUE (WORKING SET) : 0.212 \n+REMARK 3 FREE R VALUE : NULL \n+REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL \n+REMARK 3 FREE R VALUE TEST SET COUNT : NULL \n+REMARK 3 \n+REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. \n+REMARK 3 R VALUE (WORKING + TEST SET,'..b'OH A 169 22.984 29.224 13.124 0.75 22.56 O \n+HETATM 1043 O HOH A 170 30.778 7.794 -3.514 0.65 21.58 O \n+HETATM 1044 O HOH A 171 42.965 14.657 4.991 0.63 23.91 O \n+HETATM 1045 O HOH A 172 36.927 17.948 -13.093 0.62 23.36 O \n+HETATM 1046 O HOH A 173 35.412 25.852 -11.575 0.58 23.42 O \n+HETATM 1047 O HOH A 174 37.428 32.540 -5.787 0.62 21.98 O \n+HETATM 1048 O HOH A 175 37.317 8.592 7.456 0.64 22.92 O \n+HETATM 1049 O HOH A 176 9.314 36.705 -11.546 0.69 23.77 O \n+HETATM 1050 O HOH A 177 39.972 23.760 -2.655 0.86 18.96 O \n+HETATM 1051 O HOH A 178 22.128 30.274 -0.543 0.76 18.78 O \n+HETATM 1052 O HOH A 179 22.244 15.813 10.000 0.68 19.66 O \n+HETATM 1053 O HOH A 180 40.729 9.223 0.292 0.64 20.15 O \n+HETATM 1054 O HOH A 181 12.500 15.267 4.097 0.56 20.12 O \n+HETATM 1055 O HOH A 182 20.372 28.618 -2.353 0.64 20.17 O \n+HETATM 1056 O HOH A 183 22.793 15.462 -6.673 0.63 20.60 O \n+HETATM 1057 O HOH A 184 23.138 31.809 15.121 0.55 20.90 O \n+HETATM 1058 O HOH A 185 22.671 38.691 8.245 0.48 21.16 O \n+HETATM 1059 O HOH A 186 33.966 33.112 6.837 0.59 19.45 O \n+HETATM 1060 O HOH A 187 19.572 25.423 -1.420 0.53 19.94 O \n+HETATM 1061 O HOH A 188 14.790 15.672 7.259 0.52 21.22 O \n+HETATM 1062 O HOH A 189 19.112 28.022 -14.647 0.49 19.83 O \n+HETATM 1063 O HOH A 190 17.302 39.059 -12.453 0.52 20.14 O \n+HETATM 1064 O HOH A 191 16.198 14.502 5.577 0.46 20.78 O \n+HETATM 1065 O HOH A 192 17.345 46.346 -7.080 0.50 18.13 O \n+HETATM 1066 O HOH A 193 14.992 31.300 -4.242 0.46 17.90 O \n+HETATM 1067 O HOH A 194 28.196 44.775 -3.148 0.44 18.15 O \n+HETATM 1068 O HOH A 195 29.479 13.863 -9.107 0.44 18.30 O \n+HETATM 1069 O HOH A 196 23.613 44.811 2.608 0.45 17.66 O \n+HETATM 1070 O HOH A 197 40.572 22.184 -6.358 0.42 18.06 O \n+HETATM 1071 O HOH A 198 12.475 31.860 -6.226 0.47 17.85 O \n+HETATM 1072 O HOH A 199 16.684 13.594 -5.832 0.31 18.51 O \n+HETATM 1073 O HOH A 200 27.534 38.059 -12.862 0.48 18.19 O \n+HETATM 1074 O HOH A 201 25.892 35.973 11.563 0.46 18.15 O \n+HETATM 1075 O HOH A 202 24.790 25.182 16.063 0.46 17.64 O \n+HETATM 1076 O HOH A 203 12.580 21.214 5.006 0.51 17.97 O \n+HETATM 1077 O HOH A 204 19.687 23.750 -4.851 0.37 18.08 O \n+HETATM 1078 O HOH A 205 27.098 35.956 -12.358 0.39 18.71 O \n+HETATM 1079 O HOH A 206 37.255 9.634 10.002 0.46 18.39 O \n+HETATM 1080 O HOH A 207 43.755 23.843 8.038 0.38 17.96 O \n+CONECT 48 981 \n+CONECT 238 889 \n+CONECT 513 630 \n+CONECT 601 724 \n+CONECT 630 513 \n+CONECT 724 601 \n+CONECT 889 238 \n+CONECT 981 48 \n+MASTER 290 0 0 8 2 0 0 6 1079 1 8 10 \n+END \n' |
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| diff -r 000000000000 -r 69ff679edefd test-data/em.edr |
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| Binary file test-data/em.edr has changed |
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| diff -r 000000000000 -r 69ff679edefd test-data/em.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/em.gro Thu Oct 04 17:38:27 2018 -0400 |
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| b'@@ -0,0 +1,38379 @@\n+LYSOZYME in water\n+38376\n+ 1LYS N 1 4.422 3.406 2.462\n+ 1LYS H1 2 4.494 3.461 2.416\n+ 1LYS H2 3 4.354 3.379 2.393\n+ 1LYS H3 4 4.377 3.460 2.536\n+ 1LYS CA 5 4.475 3.284 2.524\n+ 1LYS HA 6 4.525 3.225 2.448\n+ 1LYS CB 7 4.578 3.317 2.635\n+ 1LYS HB1 8 4.664 3.365 2.589\n+ 1LYS HB2 9 4.537 3.390 2.705\n+ 1LYS CG 10 4.627 3.195 2.715\n+ 1LYS HG1 11 4.550 3.164 2.786\n+ 1LYS HG2 12 4.640 3.112 2.647\n+ 1LYS CD 13 4.759 3.218 2.790\n+ 1LYS HD1 14 4.838 3.237 2.718\n+ 1LYS HD2 15 4.751 3.306 2.854\n+ 1LYS CE 16 4.795 3.094 2.875\n+ 1LYS HE1 17 4.726 3.085 2.959\n+ 1LYS HE2 18 4.785 3.003 2.817\n+ 1LYS NZ 19 4.932 3.099 2.926\n+ 1LYS HZ1 20 4.942 3.016 2.986\n+ 1LYS HZ2 21 4.998 3.088 2.850\n+ 1LYS HZ3 22 4.950 3.185 2.977\n+ 1LYS C 23 4.358 3.203 2.578\n+ 1LYS O 24 4.272 3.260 2.645\n+ 2VAL N 25 4.356 3.072 2.555\n+ 2VAL H 26 4.430 3.030 2.497\n+ 2VAL CA 27 4.277 2.978 2.633\n+ 2VAL HA 28 4.200 3.028 2.690\n+ 2VAL CB 29 4.210 2.872 2.542\n+ 2VAL HB 30 4.288 2.814 2.492\n+ 2VAL CG1 31 4.121 2.775 2.623\n+ 2VAL HG11 32 4.069 2.705 2.558\n+ 2VAL HG12 33 4.179 2.716 2.694\n+ 2VAL HG13 34 4.045 2.829 2.680\n+ 2VAL CG2 35 4.125 2.937 2.432\n+ 2VAL HG21 36 4.075 2.863 2.371\n+ 2VAL HG22 37 4.049 3.000 2.477\n+ 2VAL HG23 38 4.185 3.000 2.365\n+ 2VAL C 39 4.378 2.913 2.729\n+ 2VAL O 40 4.480 2.858 2.686\n+ 3PHE N 41 4.350 2.923 2.858\n+ 3PHE H 42 4.262 2.968 2.884\n+ 3PHE CA 43 4.425 2.856 2.964\n+ 3PHE HA 44 4.532 2.858 2.942\n+ 3PHE CB 45 4.396 2.927 3.098\n+ 3PHE HB1 46 4.294 2.964 3.103\n+ 3PHE HB2 47 4.405 2.855 3.179\n+ 3PHE CG 48 4.489 3.043 3.132\n+ 3PHE CD1 49 4.468 3.171 3.079\n+ 3PHE HD1 50 4.385 3.188 3.012\n+ 3PHE CD2 51 4.595 3.021 3.221\n+ 3PHE HD2 52 4.609 2.923 3.263\n+ 3PHE CE1 53 4.556 3.276 3.112\n+ 3PHE HE1 54 4.541 3.375 3.072\n+ 3PHE CE2 55 4.683 3.126 3.256\n+ 3PHE HE2 56 4.764 3.108 3.324\n+ 3PHE CZ 57 4.663 3.254 3.200\n+ 3PHE HZ 58 4.730 3.335 3.226\n+ 3PHE C 59 4.376 2.711 2.977\n+ 3PHE O 60 4.258 2.680 2.956\n+ 4GLY N 61 4.465 2.625 3.025\n+ 4GLY H 62 4.562 2.656 3.035\n+ 4GLY CA 63 4.428 2.493 3.075\n+ 4GLY HA1 64 4.346 2.449 3.018\n+ 4GLY HA2 65 4.514 2.427 3.064\n+ 4GLY C 66 4.392 2.506 3.224\n+ 4GLY O 67 4.443 2.595 3.292\n+ 5ARG N 68 4.303 2.419 3.275\n+ 5ARG H 69 4.261 2.352 3.212\n+ 5ARG CA 70 4.249 2.422 3.412\n+ 5ARG HA 71 4.184 2.510 3.417\n+ 5ARG CB 72 4.163 2.296 3.436\n+ 5ARG HB1 73 4.079 2.296 3.367\n+ 5ARG HB2 74 4.221 2.208 3.410\n+ 5ARG CG 75 4.109 2.279 3.579\n+ 5ARG HG1 76 4.190 2.273 3.651\n+ 5ARG HG2 77 4.051 2.367 3.607\n+ 5ARG CD 78 4.021 2.154 3.596\n+ 5ARG HD1 79 3.975 2.151 3.694\n+ 5ARG HD2 80 3.938 2.157 3.525\n+ 5ARG NE 81 4.096 2.030 3.574\n+ 5ARG HE 82 4.077 1.988 3.482\n+ 5ARG CZ 83 4.166 1.961 3.666\n+ 5ARG NH1 84 4.183 2.007 3.790\n+ 5ARG HH11 85 4.151 2.100 3.820\n+ 5ARG HH12 86 4.226 1.946 3.8'..b'24 5.807\n+12240SOL OW38291 6.209 6.418 7.023\n+12240SOL HW138292 6.268 6.497 7.006\n+12240SOL HW238293 6.264 6.336 7.032\n+12241SOL OW38294 7.074 7.332 6.559\n+12241SOL HW138295 7.101 0.064 6.495\n+12241SOL HW238296 7.152 7.306 6.615\n+12242SOL OW38297 6.297 6.153 7.291\n+12242SOL HW138298 6.340 6.230 7.339\n+12242SOL HW238299 6.350 6.070 7.309\n+12243SOL OW38300 5.975 7.307 7.149\n+12243SOL HW138301 5.904 0.039 7.142\n+12243SOL HW238302 5.938 7.228 7.199\n+12244SOL OW38303 7.272 6.459 6.820\n+12244SOL HW138304 7.260 6.373 6.771\n+12244SOL HW238305 7.241 6.535 6.762\n+12245SOL OW38306 6.830 5.912 6.034\n+12245SOL HW138307 6.887 5.829 6.032\n+12245SOL HW238308 6.847 5.961 6.119\n+12246SOL OW38309 6.173 6.323 6.254\n+12246SOL HW138310 6.215 6.413 6.242\n+12246SOL HW238311 6.103 6.310 6.184\n+12247SOL OW38312 7.302 6.503 7.086\n+12247SOL HW138313 7.339 6.594 7.103\n+12247SOL HW238314 7.302 6.484 6.988\n+12248SOL OW38315 6.439 6.955 5.624\n+12248SOL HW138316 6.408 6.972 5.718\n+12248SOL HW238317 6.471 7.040 5.583\n+12249SOL OW38318 6.454 6.556 6.442\n+12249SOL HW138319 6.506 6.478 6.478\n+12249SOL HW238320 6.413 6.607 6.517\n+12250SOL OW38321 6.663 6.579 5.671\n+12250SOL HW138322 6.637 6.629 5.588\n+12250SOL HW238323 6.741 6.519 5.650\n+12251SOL OW38324 0.053 7.124 6.435\n+12251SOL HW138325 7.317 7.105 6.372\n+12251SOL HW238326 0.079 7.039 6.481\n+12252SOL OW38327 5.680 6.816 6.247\n+12252SOL HW138328 5.679 6.773 6.337\n+12252SOL HW238329 5.745 6.769 6.187\n+12253SOL OW38330 6.263 6.982 7.212\n+12253SOL HW138331 6.190 6.923 7.247\n+12253SOL HW238332 6.257 7.072 7.255\n+12254SOL OW38333 7.331 5.751 6.842\n+12254SOL HW138334 0.046 5.667 6.850\n+12254SOL HW238335 0.006 5.793 6.752\n+12255SOL OW38336 6.014 6.018 6.110\n+12255SOL HW138337 6.052 5.951 6.047\n+12255SOL HW238338 5.965 5.971 6.184\n+12256SOL OW38339 5.916 6.142 6.875\n+12256SOL HW138340 5.974 6.086 6.934\n+12256SOL HW238341 5.932 6.117 6.779\n+12257SOL OW38342 6.428 7.138 6.264\n+12257SOL HW138343 6.414 7.218 6.207\n+12257SOL HW238344 6.342 7.086 6.270\n+12258SOL OW38345 7.019 5.813 6.706\n+12258SOL HW138346 7.051 5.727 6.747\n+12258SOL HW238347 6.963 5.862 6.774\n+12259SOL OW38348 6.595 5.600 6.726\n+12259SOL HW138349 6.534 5.541 6.673\n+12259SOL HW238350 6.686 5.561 6.728\n+12260SOL OW38351 6.363 6.915 5.901\n+12260SOL HW138352 6.333 6.821 5.913\n+12260SOL HW238353 6.444 6.932 5.958\n+12261SOL OW38354 6.211 7.150 6.873\n+12261SOL HW138355 6.213 7.218 6.947\n+12261SOL HW238356 6.302 7.142 6.833\n+12262SOL OW38357 6.949 5.635 5.749\n+12262SOL HW138358 6.988 5.565 5.689\n+12262SOL HW238359 6.855 5.609 5.774\n+12263SOL OW38360 6.874 6.047 6.269\n+12263SOL HW138361 6.819 6.131 6.269\n+12263SOL HW238362 6.871 6.006 6.360\n+12264SOL OW38363 7.183 5.810 6.483\n+12264SOL HW138364 7.125 5.800 6.564\n+12264SOL HW238365 7.144 5.878 6.422\n+12265SOL OW38366 5.630 6.651 5.892\n+12265SOL HW138367 5.728 6.649 5.873\n+12265SOL HW238368 5.599 6.558 5.915\n+12266CL CL38369 0.201 2.832 1.237\n+12267CL CL38370 1.614 2.267 3.255\n+12268CL CL38371 1.597 7.226 3.986\n+12269CL CL38372 1.368 6.406 5.944\n+12270CL CL38373 3.098 3.643 6.186\n+12271CL CL38374 2.871 3.928 1.863\n+12272CL CL38375 7.226 0.967 0.588\n+12273CL CL38376 6.448 5.573 6.100\n+ 7.33925 7.33925 7.33925\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/em.tpr |
| b |
| Binary file test-data/em.tpr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/em.trr |
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| Binary file test-data/em.trr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/ions.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ions.mdp Thu Oct 04 17:38:27 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ +; ions.mdp - used as input into grompp to generate ions.tpr +; Parameters describing what to do, when to stop and what to save +integrator = steep ; Algorithm (steep = steepest descent minimization) +emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm +emstep = 0.01 ; Energy step size +nsteps = 50000 ; Maximum number of (minimization) steps to perform + +; Parameters describing how to find the neighbors of each atom and how to calculate the interactions +nstlist = 1 ; Frequency to update the neighbor list and long range forces +cutoff-scheme = Verlet +ns_type = grid ; Method to determine neighbor list (simple, grid) +coulombtype = PME ; Treatment of long range electrostatic interactions +rcoulomb = 1.0 ; Short-range electrostatic cut-off +rvdw = 1.0 ; Short-range Van der Waals cut-off +pbc = xyz ; Periodic Boundary Conditions (yes/no) |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/ions.tpr |
| b |
| Binary file test-data/ions.tpr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/md.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md.mdp Thu Oct 04 17:38:27 2018 -0400 |
| b |
| @@ -0,0 +1,46 @@ +title = OPLS Lysozyme MD simulation +; Run parameters +integrator = md ; leap-frog integrator +nsteps = 500 ; 2 * 500000 = 1000 ps (1 ns) +dt = 0.002 ; 2 fs +; Output control +nstxout = 50 ; save coordinates every 10.0 ps +nstvout = 50 ; save velocities every 10.0 ps +nstenergy = 50 ; save energies every 10.0 ps +nstlog = 50 ; update log file every 10.0 ps +nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps + ; nstxout-compressed replaces nstxtcout +compressed-x-grps = System ; replaces xtc-grps +; Bond parameters +continuation = yes ; Restarting after NPT +constraint_algorithm = lincs ; holonomic constraints +constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained +lincs_iter = 1 ; accuracy of LINCS +lincs_order = 4 ; also related to accuracy +; Neighborsearching +cutoff-scheme = Verlet +ns_type = grid ; search neighboring grid cells +nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme +rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) +rvdw = 1.0 ; short-range van der Waals cutoff (in nm) +; Electrostatics +coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics +pme_order = 4 ; cubic interpolation +fourierspacing = 0.16 ; grid spacing for FFT +; Temperature coupling is on +tcoupl = V-rescale ; modified Berendsen thermostat +tc-grps = Protein Non-Protein ; two coupling groups - more accurate +tau_t = 0.1 0.1 ; time constant, in ps +ref_t = 300 300 ; reference temperature, one for each group, in K +; Pressure coupling is on +pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT +pcoupltype = isotropic ; uniform scaling of box vectors +tau_p = 2.0 ; time constant, in ps +ref_p = 1.0 ; reference pressure, in bar +compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 +; Periodic boundary conditions +pbc = xyz ; 3-D PBC +; Dispersion correction +DispCorr = EnerPres ; account for cut-off vdW scheme +; Velocity generation +gen_vel = no ; Velocity generation is off |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/md_0_1.cpt |
| b |
| Binary file test-data/md_0_1.cpt has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/md_0_1.edr |
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| Binary file test-data/md_0_1.edr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/md_0_1.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md_0_1.gro Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,38379 @@\n+LYSOZYME in water\n+38376\n+ 1LYS N 1 4.429 3.394 2.466 0.1526 0.1131 -0.1241\n+ 1LYS H1 2 4.376 3.432 2.544 -0.2928 -0.4706 -0.1363\n+ 1LYS H2 3 4.491 3.470 2.441 -2.6019 2.5173 -0.1367\n+ 1LYS H3 4 4.371 3.381 2.385 -1.9364 0.4538 1.2296\n+ 1LYS CA 5 4.491 3.267 2.504 -0.0957 0.2396 0.7361\n+ 1LYS HA 6 4.531 3.217 2.415 0.1777 1.9459 -0.1414\n+ 1LYS CB 7 4.611 3.287 2.597 0.2331 0.3607 0.2888\n+ 1LYS HB1 8 4.691 3.335 2.540 -0.9588 0.5463 -1.3130\n+ 1LYS HB2 9 4.580 3.352 2.679 -3.1476 1.4459 -1.6371\n+ 1LYS CG 10 4.663 3.155 2.654 0.4507 0.2270 -0.2116\n+ 1LYS HG1 11 4.593 3.106 2.721 1.5678 0.1609 0.9305\n+ 1LYS HG2 12 4.691 3.078 2.582 -1.5498 -0.0941 -0.6984\n+ 1LYS CD 13 4.784 3.172 2.745 0.1335 0.5457 0.1550\n+ 1LYS HD1 14 4.879 3.175 2.692 -0.1725 -0.6211 -0.4947\n+ 1LYS HD2 15 4.778 3.262 2.806 2.1440 0.6466 0.2861\n+ 1LYS CE 16 4.789 3.047 2.833 -0.4807 -0.1214 -0.7457\n+ 1LYS HE1 17 4.719 3.047 2.917 1.7277 0.0045 1.1773\n+ 1LYS HE2 18 4.773 2.952 2.781 -0.8328 -0.4569 -0.0525\n+ 1LYS NZ 19 4.922 3.040 2.895 -0.6050 -0.3999 -0.5081\n+ 1LYS HZ1 20 4.908 2.970 2.967 -0.7211 1.5265 1.4550\n+ 1LYS HZ2 21 4.992 3.015 2.826 -0.9550 -1.2417 -0.5745\n+ 1LYS HZ3 22 4.939 3.130 2.937 1.5134 0.3689 -2.7878\n+ 1LYS C 23 4.379 3.185 2.565 0.3972 -0.1245 1.1651\n+ 1LYS O 24 4.296 3.236 2.641 -0.0875 0.6005 0.1685\n+ 2VAL N 25 4.365 3.059 2.522 0.0372 0.1665 0.4194\n+ 2VAL H 26 4.431 3.029 2.452 -1.4709 -0.4772 -0.7867\n+ 2VAL CA 27 4.289 2.960 2.595 -0.0183 0.0950 0.2651\n+ 2VAL HA 28 4.202 3.005 2.642 0.4748 -0.2845 1.5897\n+ 2VAL CB 29 4.256 2.854 2.490 -0.0649 0.4842 -0.1163\n+ 2VAL HB 30 4.351 2.822 2.447 0.5872 0.5117 1.2457\n+ 2VAL CG1 31 4.189 2.730 2.550 0.8764 0.0520 0.0663\n+ 2VAL HG11 32 4.156 2.661 2.471 0.7753 -2.7919 2.4270\n+ 2VAL HG12 33 4.265 2.675 2.605 -0.1191 -2.3114 -0.7719\n+ 2VAL HG13 34 4.102 2.763 2.607 -0.9784 -2.2582 -1.2109\n+ 2VAL CG2 35 4.170 2.914 2.378 -0.9867 -0.7006 -0.0661\n+ 2VAL HG21 36 4.167 2.847 2.293 2.5161 1.2669 -1.9884\n+ 2VAL HG22 37 4.071 2.900 2.420 -0.3698 -2.1634 1.0137\n+ 2VAL HG23 38 4.203 3.014 2.350 -0.6507 -0.3028 1.5873\n+ 2VAL C 39 4.385 2.906 2.701 0.1971 0.2163 0.1322\n+ 2VAL O 40 4.488 2.851 2.662 -0.0104 -0.1071 0.0391\n+ 3PHE N 41 4.341 2.920 2.826 -0.1972 -0.6715 0.1015\n+ 3PHE H 42 4.247 2.950 2.847 -0.6923 -1.7042 -0.5419\n+ 3PHE CA 43 4.411 2.859 2.938 0.5547 -0.1372 -0.0650\n+ 3PHE HA 44 4.519 2.861 2.932 0.5519 1.4285 0.0009\n+ 3PHE CB 45 4.372 2.945 3.058 0.1080 0.1711 -0.4294\n+ 3PHE HB1 46 4.272 2.990 3.059 0.3226 0.9335 -3.2544\n+ 3PHE HB2 47 4.372 2.886 3.149 0.6316 -0.8363 -1.0714\n+ 3PHE CG 48 4.469 3.058 3.083 -0.1237 0.2152 0.2652\n+ 3PHE CD1 49 4.451 3.178 3.014 0.0343 0.4010 0.5424\n+ 3PHE HD1 50 4.378 3.170 2.934 -0.6395 -1.6141 1.3102\n+ 3PHE CD2 51 4.576 3.051 3.172 0.0952 -0.2342 -0.0342\n+ 3PHE HD2 52 4.596 2.956 3.221 1.5937 0.9985 1.9196\n+ 3PHE CE1 53 4.529 3.294 3.030 -0.0422 0.5099 0.1465\n+ 3PHE HE1 54 4.516 3.384 2.972 -0.9626 0.9204 0.9658\n+ 3PHE CE2 55 4.661 3.160 3.191 -0.2072 -0.0117 0.0452\n+ 3PHE HE2 56 4.752 3.148 3.249 -0.2102 0.2193 0.1015\n+ 3PHE CZ 57 4.635 3'..b' 6.594 6.659 6.434 -1.7738 0.8002 -0.6626\n+12250SOL OW38321 6.642 6.652 5.572 0.4397 -0.2823 -0.0651\n+12250SOL HW138322 6.603 6.711 5.501 1.1166 -0.5859 -0.6987\n+12250SOL HW238323 6.703 6.585 5.530 -1.0446 -2.0899 0.5227\n+12251SOL OW38324 0.221 6.994 6.284 -0.4406 -0.5142 0.0142\n+12251SOL HW138325 0.151 7.017 6.216 0.0347 -1.8597 -0.9744\n+12251SOL HW238326 0.187 6.921 6.343 0.0880 -1.1555 -0.4555\n+12252SOL OW38327 5.886 6.811 6.234 0.2079 0.1277 -0.3123\n+12252SOL HW138328 5.881 6.716 6.265 -1.9732 0.6910 1.2822\n+12252SOL HW238329 5.922 6.814 6.141 -0.7392 -2.3563 -0.8212\n+12253SOL OW38330 6.262 6.835 7.257 -0.7366 -0.1839 -0.2195\n+12253SOL HW138331 6.251 6.814 7.159 0.6595 -2.7792 0.0700\n+12253SOL HW238332 6.175 6.819 7.304 -0.6013 -2.3341 -0.5780\n+12254SOL OW38333 0.052 5.676 6.899 -0.2260 0.0341 0.1024\n+12254SOL HW138334 0.052 5.713 6.806 -2.3340 0.0028 0.0399\n+12254SOL HW238335 0.036 5.751 6.964 1.0357 0.0238 0.4353\n+12255SOL OW38336 6.051 6.012 5.958 -0.4443 0.2711 -0.4477\n+12255SOL HW138337 6.125 5.979 5.899 -1.0716 0.5615 -1.4256\n+12255SOL HW238338 5.991 5.936 5.983 -0.2131 0.1575 -0.2383\n+12256SOL OW38339 5.851 5.838 6.609 0.1954 0.2156 -0.9382\n+12256SOL HW138340 5.865 5.740 6.595 0.6087 0.0502 0.5145\n+12256SOL HW238341 5.858 5.886 6.521 1.3747 -0.8889 -1.4707\n+12257SOL OW38342 6.467 7.043 6.301 -0.2687 -0.6857 -0.5813\n+12257SOL HW138343 6.397 7.030 6.231 0.6708 -0.9461 -1.5048\n+12257SOL HW238344 6.450 7.128 6.350 -2.2947 -1.6332 0.5110\n+12258SOL OW38345 6.976 5.820 6.612 -0.7520 0.3184 -0.7995\n+12258SOL HW138346 6.963 5.721 6.599 1.9691 -0.5237 1.7711\n+12258SOL HW238347 6.920 5.850 6.690 0.4183 0.1840 0.1104\n+12259SOL OW38348 6.553 5.474 6.545 -0.2222 -0.3970 -0.0364\n+12259SOL HW138349 6.539 5.397 6.483 -0.7633 0.4178 -0.9572\n+12259SOL HW238350 6.648 5.505 6.540 -0.3141 -0.2050 -0.6211\n+12260SOL OW38351 6.464 6.778 6.019 -0.0898 -0.3518 0.6137\n+12260SOL HW138352 6.429 6.686 6.036 0.1391 -0.2165 1.9489\n+12260SOL HW238353 6.554 6.788 6.061 0.4160 0.1264 -0.5369\n+12261SOL OW38354 6.399 7.017 6.835 0.6341 -0.6348 -0.3472\n+12261SOL HW138355 6.454 7.096 6.863 1.0454 -0.9700 -0.2133\n+12261SOL HW238356 6.455 6.955 6.781 -0.0284 -0.1959 -1.5896\n+12262SOL OW38357 6.886 5.508 5.832 0.1477 0.0482 0.1559\n+12262SOL HW138358 6.822 5.462 5.771 -0.1354 0.2510 0.2941\n+12262SOL HW238359 6.846 5.595 5.862 0.6586 0.3648 -0.0757\n+12263SOL OW38360 6.788 6.057 6.168 -0.0705 -0.0553 0.3629\n+12263SOL HW138361 6.693 6.087 6.161 -0.2509 -0.9176 -1.8446\n+12263SOL HW238362 6.800 6.006 6.253 -1.9423 -1.0046 0.1344\n+12264SOL OW38363 0.010 5.782 6.606 -0.6259 0.0406 0.8064\n+12264SOL HW138364 -0.089 5.789 6.606 -0.5727 1.4993 -0.1644\n+12264SOL HW238365 0.042 5.759 6.514 -0.1044 -2.0421 1.4433\n+12265SOL OW38366 5.692 6.488 5.788 -0.4835 0.1716 -0.0895\n+12265SOL HW138367 5.775 6.538 5.763 0.6221 -0.7630 1.4883\n+12265SOL HW238368 5.718 6.397 5.823 -2.0523 0.3377 1.6556\n+12266CL CL38369 7.169 2.874 1.288 -0.1056 -0.3447 0.1476\n+12267CL CL38370 1.429 2.334 3.162 -0.4813 0.1653 0.1369\n+12268CL CL38371 1.434 7.136 4.257 -0.0126 -0.1902 0.3382\n+12269CL CL38372 1.569 6.306 5.602 0.1944 -0.0930 0.0882\n+12270CL CL38373 3.048 3.765 6.004 -0.3404 -0.2297 -0.0028\n+12271CL CL38374 2.706 4.216 1.747 -0.1708 0.1789 -0.2380\n+12272CL CL38375 7.198 1.029 0.746 -0.3576 -0.3053 0.1702\n+12273CL CL38376 6.124 5.720 5.642 0.0626 -0.0337 -0.0040\n+ 7.26500 7.26500 7.26500\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/md_0_1.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md_0_1.pdb Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,38382 @@\n+TITLE LYSOZYME in water\n+REMARK THIS IS A SIMULATION BOX\n+CRYST1 72.650 72.650 72.650 90.00 90.00 90.00 P 1 1\n+MODEL 1\n+ATOM 1 N LYS 1 44.290 33.940 24.660 1.00 0.00 \n+ATOM 2 H1 LYS 1 43.760 34.320 25.440 1.00 0.00 \n+ATOM 3 H2 LYS 1 44.910 34.700 24.410 1.00 0.00 \n+ATOM 4 H3 LYS 1 43.710 33.810 23.850 1.00 0.00 \n+ATOM 5 CA LYS 1 44.910 32.670 25.040 1.00 0.00 \n+ATOM 6 HA LYS 1 45.310 32.170 24.150 1.00 0.00 \n+ATOM 7 CB LYS 1 46.110 32.870 25.970 1.00 0.00 \n+ATOM 8 HB1 LYS 1 46.910 33.350 25.400 1.00 0.00 \n+ATOM 9 HB2 LYS 1 45.800 33.520 26.790 1.00 0.00 \n+ATOM 10 CG LYS 1 46.630 31.550 26.540 1.00 0.00 \n+ATOM 11 HG1 LYS 1 45.930 31.060 27.210 1.00 0.00 \n+ATOM 12 HG2 LYS 1 46.910 30.780 25.820 1.00 0.00 \n+ATOM 13 CD LYS 1 47.840 31.720 27.450 1.00 0.00 \n+ATOM 14 HD1 LYS 1 48.790 31.750 26.920 1.00 0.00 \n+ATOM 15 HD2 LYS 1 47.780 32.620 28.060 1.00 0.00 \n+ATOM 16 CE LYS 1 47.890 30.470 28.330 1.00 0.00 \n+ATOM 17 HE1 LYS 1 47.190 30.470 29.170 1.00 0.00 \n+ATOM 18 HE2 LYS 1 47.730 29.520 27.810 1.00 0.00 \n+ATOM 19 NZ LYS 1 49.220 30.400 28.950 1.00 0.00 \n+ATOM 20 HZ1 LYS 1 49.080 29.700 29.670 1.00 0.00 \n+ATOM 21 HZ2 LYS 1 49.920 30.150 28.260 1.00 0.00 \n+ATOM 22 HZ3 LYS 1 49.390 31.300 29.370 1.00 0.00 \n+ATOM 23 C LYS 1 43.790 31.850 25.650 1.00 0.00 \n+ATOM 24 O LYS 1 42.960 32.360 26.410 1.00 0.00 \n+ATOM 25 N VAL 2 43.650 30.590 25.220 1.00 0.00 \n+ATOM 26 H VAL 2 44.310 30.290 24.520 1.00 0.00 \n+ATOM 27 CA VAL 2 42.890 29.600 25.950 1.00 0.00 \n+ATOM 28 HA VAL 2 42.020 30.050 26.420 1.00 0.00 \n+ATOM 29 CB VAL 2 42.560 28.540 24.900 1.00 0.00 \n+ATOM 30 HB VAL 2 43.510 28.220 24.470 1.00 0.00 \n+ATOM 31 CG1 VAL 2 41.890 27.300 25.500 1.00 0.00 \n+ATOM 32 1HG1 VAL 2 41.560 26.610 24.710 1.00 0.00 \n+ATOM 33 2HG1 VAL 2 42.650 26.750 26.050 1.00 0.00 \n+ATOM 34 3HG1 VAL 2 41.020 27.630 26.070 1.00 0.00 \n+ATOM 35 CG2 VAL 2 41.700 29.140 23.780 1.00 0.00 \n+ATOM 36 1HG2 VAL 2 41.670 28.470 22.930 1.00 0.00 \n+ATOM 37 2HG2 VAL 2 40.710 29.000 24.200 1.00 0.00 \n+ATOM 38 3HG2 VAL 2 42.030 30.140 23.500 1.00 0.00 \n+ATOM 39 C VAL 2 43.850 29.060 27.010 1.00 0.00 \n+ATOM 40 O VAL 2 44.880 28.510 26.620 1.00 0.00 \n+ATOM 41 N PHE 3 43.410 29.200 28.260 1.00 0.00 \n+ATOM 42 H PHE 3 42.470 29.500 28.470 1.00 0.00 \n+ATOM 43 CA PHE 3 44.110 28.590 29.380 1.00 0.00 \n+ATOM 44 HA PHE 3 45.190 28.610 29.320 1.00 0.00 \n+ATOM 45 CB PHE 3 43.720 29.450 30.580 1.00 0.00 \n+ATOM 46 HB1 PHE 3 42.720 29.900 30.590 1.00 0.00 \n+ATOM 47 HB2 PHE 3 43.720 28.860 31.490 1.00 0.00 \n+ATOM 48 CG PHE 3 44.690 30.580 30.830 1.00 0.0'..b'OW SOL 2252 58.860 68.110 62.340 1.00 0.00 \n+ATOM 38328 HW1 SOL 2252 58.810 67.160 62.650 1.00 0.00 \n+ATOM 38329 HW2 SOL 2252 59.220 68.140 61.410 1.00 0.00 \n+ATOM 38330 OW SOL 2253 62.620 68.350 72.570 1.00 0.00 \n+ATOM 38331 HW1 SOL 2253 62.510 68.140 71.590 1.00 0.00 \n+ATOM 38332 HW2 SOL 2253 61.750 68.190 73.040 1.00 0.00 \n+ATOM 38333 OW SOL 2254 0.520 56.760 68.990 1.00 0.00 \n+ATOM 38334 HW1 SOL 2254 0.520 57.130 68.060 1.00 0.00 \n+ATOM 38335 HW2 SOL 2254 0.360 57.510 69.640 1.00 0.00 \n+ATOM 38336 OW SOL 2255 60.510 60.120 59.580 1.00 0.00 \n+ATOM 38337 HW1 SOL 2255 61.250 59.790 58.990 1.00 0.00 \n+ATOM 38338 HW2 SOL 2255 59.910 59.360 59.830 1.00 0.00 \n+ATOM 38339 OW SOL 2256 58.510 58.380 66.090 1.00 0.00 \n+ATOM 38340 HW1 SOL 2256 58.650 57.400 65.950 1.00 0.00 \n+ATOM 38341 HW2 SOL 2256 58.580 58.860 65.210 1.00 0.00 \n+ATOM 38342 OW SOL 2257 64.670 70.430 63.010 1.00 0.00 \n+ATOM 38343 HW1 SOL 2257 63.970 70.300 62.310 1.00 0.00 \n+ATOM 38344 HW2 SOL 2257 64.500 71.280 63.500 1.00 0.00 \n+ATOM 38345 OW SOL 2258 69.760 58.200 66.120 1.00 0.00 \n+ATOM 38346 HW1 SOL 2258 69.630 57.210 65.990 1.00 0.00 \n+ATOM 38347 HW2 SOL 2258 69.200 58.500 66.900 1.00 0.00 \n+ATOM 38348 OW SOL 2259 65.530 54.740 65.450 1.00 0.00 \n+ATOM 38349 HW1 SOL 2259 65.390 53.970 64.830 1.00 0.00 \n+ATOM 38350 HW2 SOL 2259 66.480 55.050 65.400 1.00 0.00 \n+ATOM 38351 OW SOL 2260 64.640 67.780 60.190 1.00 0.00 \n+ATOM 38352 HW1 SOL 2260 64.290 66.860 60.360 1.00 0.00 \n+ATOM 38353 HW2 SOL 2260 65.540 67.880 60.610 1.00 0.00 \n+ATOM 38354 OW SOL 2261 63.990 70.170 68.350 1.00 0.00 \n+ATOM 38355 HW1 SOL 2261 64.540 70.960 68.630 1.00 0.00 \n+ATOM 38356 HW2 SOL 2261 64.550 69.550 67.810 1.00 0.00 \n+ATOM 38357 OW SOL 2262 68.860 55.080 58.320 1.00 0.00 \n+ATOM 38358 HW1 SOL 2262 68.220 54.620 57.710 1.00 0.00 \n+ATOM 38359 HW2 SOL 2262 68.460 55.950 58.620 1.00 0.00 \n+ATOM 38360 OW SOL 2263 67.880 60.570 61.680 1.00 0.00 \n+ATOM 38361 HW1 SOL 2263 66.930 60.870 61.610 1.00 0.00 \n+ATOM 38362 HW2 SOL 2263 68.000 60.060 62.530 1.00 0.00 \n+ATOM 38363 OW SOL 2264 0.100 57.820 66.060 1.00 0.00 \n+ATOM 38364 HW1 SOL 2264 -0.890 57.890 66.060 1.00 0.00 \n+ATOM 38365 HW2 SOL 2264 0.420 57.590 65.140 1.00 0.00 \n+ATOM 38366 OW SOL 2265 56.920 64.880 57.880 1.00 0.00 \n+ATOM 38367 HW1 SOL 2265 57.750 65.380 57.630 1.00 0.00 \n+ATOM 38368 HW2 SOL 2265 57.180 63.970 58.230 1.00 0.00 \n+ATOM 38369 CL CL 2266 71.690 28.740 12.880 1.00 0.00 \n+ATOM 38370 CL CL 2267 14.290 23.340 31.620 1.00 0.00 \n+ATOM 38371 CL CL 2268 14.340 71.360 42.570 1.00 0.00 \n+ATOM 38372 CL CL 2269 15.690 63.060 56.020 1.00 0.00 \n+ATOM 38373 CL CL 2270 30.480 37.650 60.040 1.00 0.00 \n+ATOM 38374 CL CL 2271 27.060 42.160 17.470 1.00 0.00 \n+ATOM 38375 CL CL 2272 71.980 10.290 7.460 1.00 0.00 \n+ATOM 38376 CL CL 2273 61.240 57.200 56.420 1.00 0.00 \n+TER\n+ENDMDL\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/md_0_1.tpr |
| b |
| Binary file test-data/md_0_1.tpr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/md_0_1.trr |
| b |
| Binary file test-data/md_0_1.trr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/md_0_1.xtc |
| b |
| Binary file test-data/md_0_1.xtc has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/minim.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minim.mdp Thu Oct 04 17:38:27 2018 -0400 |
| b |
| @@ -0,0 +1,14 @@ +; minim.mdp - used as input into grompp to generate em.tpr +integrator = steep ; Algorithm (steep = steepest descent minimization) +emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm +emstep = 0.01 ; Energy step size +nsteps = 50000 ; Maximum number of (minimization) steps to perform + +; Parameters describing how to find the neighbors of each atom and how to calculate the interactions +nstlist = 1 ; Frequency to update the neighbor list and long range forces +cutoff-scheme = Verlet +ns_type = grid ; Method to determine neighbor list (simple, grid) +coulombtype = PME ; Treatment of long range electrostatic interactions +rcoulomb = 1.0 ; Short-range electrostatic cut-off +rvdw = 1.0 ; Short-range Van der Waals cut-off +pbc = xyz ; Periodic Boundary Conditions (yes/no) |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/newbox.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/newbox.gro Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,2197 @@\n+LYSOZYME\n+ 2194\n+ 1LYS N 1 4.434 3.396 2.469\n+ 1LYS H1 2 4.510 3.450 2.431\n+ 1LYS H2 3 4.368 3.376 2.397\n+ 1LYS H3 4 4.390 3.448 2.542\n+ 1LYS CA 5 4.487 3.269 2.524\n+ 1LYS HA 6 4.531 3.217 2.451\n+ 1LYS CB 7 4.585 3.306 2.636\n+ 1LYS HB1 8 4.661 3.357 2.597\n+ 1LYS HB2 9 4.537 3.363 2.703\n+ 1LYS CG 10 4.643 3.187 2.711\n+ 1LYS HG1 11 4.574 3.151 2.773\n+ 1LYS HG2 12 4.668 3.116 2.644\n+ 1LYS CD 13 4.767 3.227 2.790\n+ 1LYS HD1 14 4.843 3.245 2.727\n+ 1LYS HD2 15 4.747 3.309 2.843\n+ 1LYS CE 16 4.804 3.113 2.883\n+ 1LYS HE1 17 4.739 3.108 2.959\n+ 1LYS HE2 18 4.804 3.026 2.834\n+ 1LYS NZ 19 4.940 3.139 2.937\n+ 1LYS HZ1 20 4.967 3.065 2.999\n+ 1LYS HZ2 21 5.006 3.144 2.861\n+ 1LYS HZ3 22 4.940 3.226 2.987\n+ 1LYS C 23 4.372 3.188 2.583\n+ 1LYS O 24 4.293 3.243 2.659\n+ 2VAL N 25 4.372 3.058 2.563\n+ 2VAL H 26 4.434 3.022 2.493\n+ 2VAL CA 27 4.288 2.962 2.634\n+ 2VAL HA 28 4.215 3.014 2.677\n+ 2VAL CB 29 4.212 2.865 2.544\n+ 2VAL HB 30 4.284 2.814 2.497\n+ 2VAL CG1 31 4.123 2.770 2.624\n+ 2VAL HG11 32 4.075 2.709 2.561\n+ 2VAL HG12 33 4.180 2.717 2.686\n+ 2VAL HG13 34 4.056 2.823 2.676\n+ 2VAL CG2 35 4.127 2.933 2.438\n+ 2VAL HG21 36 4.081 2.864 2.383\n+ 2VAL HG22 37 4.060 2.992 2.482\n+ 2VAL HG23 38 4.186 2.989 2.379\n+ 2VAL C 39 4.378 2.893 2.738\n+ 2VAL O 40 4.474 2.823 2.701\n+ 3PHE N 41 4.347 2.917 2.863\n+ 3PHE H 42 4.273 2.981 2.883\n+ 3PHE CA 43 4.417 2.852 2.975\n+ 3PHE HA 44 4.513 2.859 2.950\n+ 3PHE CB 45 4.395 2.925 3.108\n+ 3PHE HB1 46 4.303 2.964 3.109\n+ 3PHE HB2 47 4.404 2.860 3.183\n+ 3PHE CG 48 4.492 3.036 3.129\n+ 3PHE CD1 49 4.465 3.167 3.087\n+ 3PHE HD1 50 4.379 3.187 3.040\n+ 3PHE CD2 51 4.598 3.018 3.220\n+ 3PHE HD2 52 4.611 2.928 3.262\n+ 3PHE CE1 53 4.556 3.270 3.110\n+ 3PHE HE1 54 4.546 3.357 3.063\n+ 3PHE CE2 55 4.685 3.121 3.251\n+ 3PHE HE2 56 4.764 3.104 3.310\n+ 3PHE CZ 57 4.662 3.249 3.200\n+ 3PHE HZ 58 4.720 3.326 3.228\n+ 3PHE C 59 4.372 2.706 2.990\n+ 3PHE O 60 4.250 2.678 2.981\n+ 4GLY N 61 4.470 2.626 3.034\n+ 4GLY H 62 4.565 2.657 3.035\n+ 4GLY CA 63 4.435 2.490 3.080\n+ 4GLY HA1 64 4.360 2.454 3.024\n+ 4GLY HA2 65 4.514 2.430 3.073\n+ 4GLY C 66 4.390 2.504 3.225\n+ 4GLY O 67 4.428 2.602 3.289\n+ 5ARG N 68 4.303 2.416 3.270\n+ 5ARG H 69 4.269 2.346 3.207\n+ 5ARG CA 70 4.254 2.416 3.408\n+ 5ARG HA 71 4.196 2.496 3.415\n+ 5ARG CB 72 4.174 2.288 3.434\n+ 5ARG HB1 73 4.098 2.284 3.370\n+ 5ARG HB2 74 4.234 2.209 3.420\n+ 5ARG CG 75 4.119 2.282 3.575\n+ 5ARG HG1 76 4.195 2.279 3.640\n+ 5ARG HG2 77 4.063 2.363 3.592\n+ 5ARG CD 78 4.036 2.162 3.595\n+ 5ARG HD1 79 4.002 2.161 3.689\n+ 5ARG HD2 80 3.958 2.167 3.532\n+ 5ARG NE 81 4.104 2.037 3.571\n+ 5ARG HE 82 4.100 2.002 3.478\n+ 5ARG CZ 83 4.171 1.963 3.657\n+ 5ARG NH1 84 4.182 1.995 3.786\n+ 5ARG HH11 85 4.137 2.078 3.820\n+ 5ARG HH12 86 4.234 1.937 3.848\n+ 5A'..b'43 4.667\n+ 179HOH HW1 2109 3.204 2.743 4.725\n+ 179HOH HW2 2110 3.122 2.825 4.609\n+ 180HOH OW 2111 4.971 2.084 3.696\n+ 180HOH HW1 2112 5.053 2.084 3.754\n+ 180HOH HW2 2113 4.971 2.003 3.638\n+ 181HOH OW 2114 2.148 2.689 4.077\n+ 181HOH HW1 2115 2.066 2.689 4.134\n+ 181HOH HW2 2116 2.148 2.770 4.019\n+ 182HOH OW 2117 2.935 4.024 3.432\n+ 182HOH HW1 2118 2.854 4.024 3.489\n+ 182HOH HW2 2119 2.935 3.942 3.374\n+ 183HOH OW 2120 3.177 2.708 3.000\n+ 183HOH HW1 2121 3.177 2.790 2.942\n+ 183HOH HW2 2122 3.177 2.627 2.942\n+ 184HOH OW 2123 3.212 4.343 5.179\n+ 184HOH HW1 2124 3.293 4.343 5.237\n+ 184HOH HW2 2125 3.130 4.343 5.237\n+ 185HOH OW 2126 3.165 5.031 4.492\n+ 185HOH HW1 2127 3.247 5.031 4.549\n+ 185HOH HW2 2128 3.165 5.113 4.434\n+ 186HOH OW 2129 4.295 4.473 4.351\n+ 186HOH HW1 2130 4.376 4.473 4.408\n+ 186HOH HW2 2131 4.295 4.392 4.293\n+ 187HOH OW 2132 2.855 3.704 3.525\n+ 187HOH HW1 2133 2.774 3.704 3.583\n+ 187HOH HW2 2134 2.855 3.786 3.467\n+ 188HOH OW 2135 2.377 2.729 4.393\n+ 188HOH HW1 2136 2.295 2.729 4.451\n+ 188HOH HW2 2137 2.377 2.648 4.335\n+ 189HOH OW 2138 2.809 3.964 2.202\n+ 189HOH HW1 2139 2.809 4.046 2.145\n+ 189HOH HW2 2140 2.809 3.883 2.145\n+ 190HOH OW 2141 2.628 5.068 2.422\n+ 190HOH HW1 2142 2.710 5.068 2.479\n+ 190HOH HW2 2143 2.547 5.068 2.479\n+ 191HOH OW 2144 2.518 2.612 4.225\n+ 191HOH HW1 2145 2.599 2.612 4.282\n+ 191HOH HW2 2146 2.518 2.694 4.167\n+ 192HOH OW 2147 2.633 5.797 2.959\n+ 192HOH HW1 2148 2.714 5.797 3.017\n+ 192HOH HW2 2149 2.633 5.715 2.901\n+ 193HOH OW 2150 2.397 4.292 3.243\n+ 193HOH HW1 2151 2.316 4.292 3.301\n+ 193HOH HW2 2152 2.397 4.374 3.185\n+ 194HOH OW 2153 3.718 5.639 3.352\n+ 194HOH HW1 2154 3.636 5.639 3.410\n+ 194HOH HW2 2155 3.718 5.558 3.294\n+ 195HOH OW 2156 3.846 2.548 2.756\n+ 195HOH HW1 2157 3.846 2.630 2.699\n+ 195HOH HW2 2158 3.846 2.467 2.699\n+ 196HOH OW 2159 3.259 5.643 3.928\n+ 196HOH HW1 2160 3.341 5.643 3.986\n+ 196HOH HW2 2161 3.178 5.643 3.986\n+ 197HOH OW 2162 4.955 3.380 3.031\n+ 197HOH HW1 2163 5.037 3.380 3.089\n+ 197HOH HW2 2164 4.955 3.462 2.973\n+ 198HOH OW 2165 2.145 4.348 3.044\n+ 198HOH HW1 2166 2.227 4.348 3.102\n+ 198HOH HW2 2167 2.145 4.266 2.987\n+ 199HOH OW 2168 2.566 2.521 3.084\n+ 199HOH HW1 2169 2.485 2.521 3.142\n+ 199HOH HW2 2170 2.566 2.603 3.026\n+ 200HOH OW 2171 3.651 4.968 2.381\n+ 200HOH HW1 2172 3.570 4.968 2.439\n+ 200HOH HW2 2173 3.651 4.886 2.323\n+ 201HOH OW 2174 3.487 4.759 4.823\n+ 201HOH HW1 2175 3.487 4.841 4.766\n+ 201HOH HW2 2176 3.487 4.678 4.766\n+ 202HOH OW 2177 3.377 3.680 5.273\n+ 202HOH HW1 2178 3.459 3.680 5.331\n+ 202HOH HW2 2179 3.295 3.680 5.331\n+ 203HOH OW 2180 2.156 3.283 4.168\n+ 203HOH HW1 2181 2.238 3.283 4.225\n+ 203HOH HW2 2182 2.156 3.365 4.110\n+ 204HOH OW 2183 2.867 3.537 3.182\n+ 204HOH HW1 2184 2.948 3.537 3.240\n+ 204HOH HW2 2185 2.867 3.455 3.124\n+ 205HOH OW 2186 3.608 4.758 2.431\n+ 205HOH HW1 2187 3.526 4.758 2.489\n+ 205HOH HW2 2188 3.608 4.839 2.373\n+ 206HOH OW 2189 4.624 2.125 4.667\n+ 206HOH HW1 2190 4.542 2.125 4.725\n+ 206HOH HW2 2191 4.624 2.044 4.609\n+ 207HOH OW 2192 5.274 3.546 4.471\n+ 207HOH HW1 2193 5.274 3.628 4.413\n+ 207HOH HW2 2194 5.274 3.465 4.413\n+ 7.33925 7.33925 7.33925\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/npt.cpt |
| b |
| Binary file test-data/npt.cpt has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/npt.edr |
| b |
| Binary file test-data/npt.edr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/npt.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/npt.gro Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,38379 @@\n+LYSOZYME in water\n+38376\n+ 1LYS N 1 4.408 3.350 2.380 0.2673 -0.2389 -0.2411\n+ 1LYS H1 2 4.357 3.419 2.434 -2.0147 -3.2163 1.6987\n+ 1LYS H2 3 4.495 3.391 2.348 1.8056 0.2972 3.9647\n+ 1LYS H3 4 4.344 3.328 2.306 0.1919 1.7185 -0.8172\n+ 1LYS CA 5 4.451 3.234 2.460 -0.1814 -0.2864 -0.0670\n+ 1LYS HA 6 4.495 3.159 2.394 -0.9330 -0.3806 -0.4691\n+ 1LYS CB 7 4.551 3.281 2.565 0.1538 -0.6499 -0.2213\n+ 1LYS HB1 8 4.640 3.316 2.511 1.2282 -2.7628 0.0889\n+ 1LYS HB2 9 4.520 3.359 2.635 -0.3923 -1.0803 0.0156\n+ 1LYS CG 10 4.604 3.165 2.650 -0.5902 -0.7915 0.0569\n+ 1LYS HG1 11 4.520 3.134 2.712 0.0041 -0.3176 1.1209\n+ 1LYS HG2 12 4.625 3.080 2.585 -3.7650 -2.9660 1.6442\n+ 1LYS CD 13 4.734 3.179 2.730 -0.3604 0.0504 -0.4451\n+ 1LYS HD1 14 4.812 3.206 2.659 -1.4519 0.7539 -1.4277\n+ 1LYS HD2 15 4.724 3.268 2.791 -1.4094 -0.0837 -0.3945\n+ 1LYS CE 16 4.765 3.053 2.810 -0.0162 0.2836 -0.2114\n+ 1LYS HE1 17 4.694 3.036 2.892 0.2672 1.6909 0.3608\n+ 1LYS HE2 18 4.766 2.970 2.740 0.7349 -0.9581 1.2064\n+ 1LYS NZ 19 4.895 3.062 2.879 0.0455 -0.1023 -0.2723\n+ 1LYS HZ1 20 4.894 2.991 2.951 1.0000 0.2530 0.1086\n+ 1LYS HZ2 21 4.975 3.032 2.826 0.6308 -0.7796 0.9448\n+ 1LYS HZ3 22 4.913 3.152 2.922 0.7111 0.5100 -1.7730\n+ 1LYS C 23 4.325 3.170 2.517 -0.5645 -0.0792 -0.6703\n+ 1LYS O 24 4.226 3.236 2.549 -0.0598 -0.1994 1.2613\n+ 2VAL N 25 4.331 3.038 2.535 0.0240 -0.0274 -0.4489\n+ 2VAL H 26 4.420 2.998 2.510 -0.8414 -1.3266 -1.6119\n+ 2VAL CA 27 4.240 2.953 2.609 0.2149 0.2665 0.1264\n+ 2VAL HA 28 4.160 3.010 2.657 -0.6507 -1.0888 0.3432\n+ 2VAL CB 29 4.181 2.848 2.515 -0.2871 0.3076 0.3915\n+ 2VAL HB 30 4.253 2.767 2.498 -0.4883 -0.0324 1.1057\n+ 2VAL CG1 31 4.065 2.780 2.588 -0.2564 0.4922 0.6151\n+ 2VAL HG11 32 4.037 2.684 2.543 2.0462 0.4271 -0.8292\n+ 2VAL HG12 33 4.085 2.758 2.693 -0.9377 -0.1345 0.6214\n+ 2VAL HG13 34 3.985 2.853 2.581 2.6126 3.9598 1.0909\n+ 2VAL CG2 35 4.142 2.901 2.377 -1.3893 -0.3679 0.4355\n+ 2VAL HG21 36 4.077 2.844 2.311 -0.0228 1.5345 -2.7632\n+ 2VAL HG22 37 4.091 2.996 2.396 -1.1628 -0.2118 0.2568\n+ 2VAL HG23 38 4.237 2.911 2.325 -2.5287 0.3993 -1.6123\n+ 2VAL C 39 4.337 2.883 2.702 -0.0739 0.1915 0.3728\n+ 2VAL O 40 4.423 2.805 2.660 0.0168 0.5114 -0.0361\n+ 3PHE N 41 4.324 2.898 2.834 0.4011 0.3011 0.4101\n+ 3PHE H 42 4.247 2.956 2.866 -0.4593 -1.0557 0.8615\n+ 3PHE CA 43 4.407 2.826 2.928 0.1485 -0.1812 0.2640\n+ 3PHE HA 44 4.513 2.821 2.903 0.5097 1.3630 1.3490\n+ 3PHE CB 45 4.397 2.899 3.061 -0.4077 0.1099 0.0651\n+ 3PHE HB1 46 4.294 2.926 3.082 -0.0300 0.5989 1.4607\n+ 3PHE HB2 47 4.404 2.836 3.150 -3.4703 0.1153 0.4218\n+ 3PHE CG 48 4.497 3.011 3.081 0.4838 -0.6720 0.0844\n+ 3PHE CD1 49 4.463 3.134 3.023 -0.0940 -0.5337 0.6872\n+ 3PHE HD1 50 4.374 3.148 2.963 1.6637 1.6586 -1.6592\n+ 3PHE CD2 51 4.616 2.997 3.153 0.3845 -0.0950 0.3680\n+ 3PHE HD2 52 4.640 2.901 3.195 1.4596 0.5525 1.3091\n+ 3PHE CE1 53 4.552 3.242 3.036 -0.0893 -0.4264 -0.1459\n+ 3PHE HE1 54 4.529 3.337 2.991 2.1152 0.4609 0.4758\n+ 3PHE CE2 55 4.706 3.103 3.170 0.5168 -0.1509 0.0046\n+ 3PHE HE2 56 4.794 3.086 3.231 1.5562 0.8793 -1.1371\n+ 3PHE CZ 57 4.667 3'..b' 6.534 6.752 6.417 1.7065 1.2735 0.6150\n+12250SOL OW38321 6.610 6.507 5.569 -0.2728 -0.1084 -0.1351\n+12250SOL HW138322 6.517 6.517 5.533 -1.0857 -1.3245 1.5147\n+12250SOL HW238323 6.675 6.508 5.493 -1.7304 -0.4547 -1.4407\n+12251SOL OW38324 0.186 7.031 6.218 -0.6592 0.1133 -0.0367\n+12251SOL HW138325 0.161 7.110 6.163 1.0967 0.9411 0.2712\n+12251SOL HW238326 0.157 7.045 6.313 1.7475 1.6096 0.5887\n+12252SOL OW38327 5.889 6.874 6.297 0.4970 0.3503 0.6455\n+12252SOL HW138328 5.911 6.789 6.345 1.2298 0.6690 0.9050\n+12252SOL HW238329 5.872 6.855 6.201 -2.5854 -0.5329 1.2610\n+12253SOL OW38330 6.263 6.948 7.183 0.3513 0.0813 0.2792\n+12253SOL HW138331 6.268 6.958 7.084 -0.7020 -1.8778 -0.0173\n+12253SOL HW238332 6.174 6.981 7.216 0.6997 0.7326 0.5799\n+12254SOL OW38333 0.087 5.675 6.743 0.5294 -0.6303 0.5136\n+12254SOL HW138334 0.086 5.662 6.644 1.7224 -2.0435 0.6554\n+12254SOL HW238335 0.142 5.756 6.765 -2.1682 1.5070 -0.0784\n+12255SOL OW38336 5.982 5.966 5.990 0.6792 0.8327 -0.0442\n+12255SOL HW138337 6.064 5.944 5.936 -0.0320 -0.3348 -0.6870\n+12255SOL HW238338 5.950 5.883 6.037 0.8030 1.6439 1.5495\n+12256SOL OW38339 5.920 5.931 6.681 0.3649 -0.8352 -0.8726\n+12256SOL HW138340 5.861 5.859 6.646 -1.6541 0.4543 -0.2571\n+12256SOL HW238341 5.912 6.012 6.624 1.5926 -0.6285 -0.7828\n+12257SOL OW38342 6.474 7.176 6.127 0.3088 -0.0462 0.4559\n+12257SOL HW138343 6.422 7.188 6.042 0.3146 -2.2977 0.0860\n+12257SOL HW238344 6.416 7.133 6.196 0.9544 -0.2926 0.8559\n+12258SOL OW38345 7.041 5.832 6.601 -0.2064 0.5007 1.0587\n+12258SOL HW138346 7.031 5.744 6.647 4.5585 -0.4130 0.8280\n+12258SOL HW238347 7.044 5.905 6.670 -1.8123 0.2866 1.4081\n+12259SOL OW38348 6.801 5.545 6.492 -0.7350 -0.1021 0.1004\n+12259SOL HW138349 6.774 5.449 6.480 -4.3535 0.7938 -0.0622\n+12259SOL HW238350 6.869 5.551 6.565 1.2416 -2.9467 -1.3287\n+12260SOL OW38351 6.427 6.776 5.886 0.3472 -0.0778 0.3187\n+12260SOL HW138352 6.408 6.684 5.919 2.9787 -1.4486 -1.5641\n+12260SOL HW238353 6.526 6.792 5.886 0.0183 2.4123 -0.3067\n+12261SOL OW38354 6.486 7.169 6.761 0.5917 0.1406 -0.1300\n+12261SOL HW138355 6.538 7.230 6.821 0.2500 -1.6364 2.1028\n+12261SOL HW238356 6.549 7.107 6.714 0.7375 0.3900 -0.2676\n+12262SOL OW38357 6.897 5.563 5.966 0.0143 0.2020 -0.8573\n+12262SOL HW138358 6.857 5.545 5.876 -2.3214 0.4239 0.0732\n+12262SOL HW238359 6.861 5.648 6.002 -1.7036 -1.4650 1.6365\n+12263SOL OW38360 6.734 6.086 6.239 -0.3380 -0.2278 0.4357\n+12263SOL HW138361 6.637 6.061 6.233 -0.7993 1.2854 1.0226\n+12263SOL HW238362 6.765 6.076 6.334 0.2472 -1.2083 0.1568\n+12264SOL OW38363 7.257 5.723 6.475 -0.4119 -0.1596 0.0997\n+12264SOL HW138364 7.200 5.784 6.531 0.9150 1.0201 0.2114\n+12264SOL HW238365 7.218 5.717 6.383 -1.5977 -0.6640 0.6141\n+12265SOL OW38366 5.636 6.430 5.796 0.8169 -0.0958 -0.1490\n+12265SOL HW138367 5.705 6.496 5.822 0.9752 -0.6747 0.9604\n+12265SOL HW238368 5.617 6.369 5.873 -0.0086 -0.7444 -0.8397\n+12266CL CL38369 0.046 2.908 1.329 -0.2298 -0.3149 -0.1369\n+12267CL CL38370 1.513 2.405 3.178 -0.3140 -0.0194 -0.3672\n+12268CL CL38371 1.503 7.246 4.172 -0.2315 0.0180 0.2176\n+12269CL CL38372 1.523 6.364 5.741 -0.0948 -0.2998 0.2157\n+12270CL CL38373 3.021 3.714 6.119 0.0026 -0.4095 -0.0198\n+12271CL CL38374 2.756 4.105 1.673 -0.1828 0.2375 -0.1030\n+12272CL CL38375 0.038 1.035 0.677 -0.1162 -0.0511 -0.4826\n+12273CL CL38376 6.261 5.675 5.710 -0.4433 -0.0837 -0.0991\n+ 7.25935 7.25935 7.25935\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/npt.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/npt.mdp Thu Oct 04 17:38:27 2018 -0400 |
| b |
| @@ -0,0 +1,46 @@ +title = OPLS Lysozyme NPT equilibration +define = -DPOSRES ; position restrain the protein +; Run parameters +integrator = md ; leap-frog integrator +nsteps = 500 ; 2 * 50000 = 100 ps +dt = 0.002 ; 2 fs +; Output control +nstxout = 50 ; save coordinates every 1.0 ps +nstvout = 50 ; save velocities every 1.0 ps +nstenergy = 50 ; save energies every 1.0 ps +nstlog = 50 ; update log file every 1.0 ps +nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps +; Bond parameters +continuation = yes ; Restarting after NVT +constraint_algorithm = lincs ; holonomic constraints +constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained +lincs_iter = 1 ; accuracy of LINCS +lincs_order = 4 ; also related to accuracy +; Neighborsearching +cutoff-scheme = Verlet +ns_type = grid ; search neighboring grid cells +nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme +rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) +rvdw = 1.0 ; short-range van der Waals cutoff (in nm) +; Electrostatics +coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics +pme_order = 4 ; cubic interpolation +fourierspacing = 0.16 ; grid spacing for FFT +; Temperature coupling is on +tcoupl = V-rescale ; modified Berendsen thermostat +tc-grps = Protein Non-Protein ; two coupling groups - more accurate +tau_t = 0.1 0.1 ; time constant, in ps +ref_t = 300 300 ; reference temperature, one for each group, in K +; Pressure coupling is on +pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT +pcoupltype = isotropic ; uniform scaling of box vectors +tau_p = 2.0 ; time constant, in ps +ref_p = 1.0 ; reference pressure, in bar +compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 +refcoord_scaling = com +; Periodic boundary conditions +pbc = xyz ; 3-D PBC +; Dispersion correction +DispCorr = EnerPres ; account for cut-off vdW scheme +; Velocity generation +gen_vel = no ; Velocity generation is off |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/npt.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/npt.pdb Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,38382 @@\n+TITLE LYSOZYME in water\n+REMARK THIS IS A SIMULATION BOX\n+CRYST1 72.593 72.593 72.593 90.00 90.00 90.00 P 1 1\n+MODEL 1\n+ATOM 1 N LYS 1 44.080 33.500 23.800 1.00 0.00 \n+ATOM 2 H1 LYS 1 43.570 34.190 24.340 1.00 0.00 \n+ATOM 3 H2 LYS 1 44.950 33.910 23.480 1.00 0.00 \n+ATOM 4 H3 LYS 1 43.440 33.280 23.060 1.00 0.00 \n+ATOM 5 CA LYS 1 44.510 32.340 24.600 1.00 0.00 \n+ATOM 6 HA LYS 1 44.950 31.590 23.940 1.00 0.00 \n+ATOM 7 CB LYS 1 45.510 32.810 25.650 1.00 0.00 \n+ATOM 8 HB1 LYS 1 46.400 33.160 25.110 1.00 0.00 \n+ATOM 9 HB2 LYS 1 45.200 33.590 26.350 1.00 0.00 \n+ATOM 10 CG LYS 1 46.040 31.650 26.500 1.00 0.00 \n+ATOM 11 HG1 LYS 1 45.200 31.340 27.120 1.00 0.00 \n+ATOM 12 HG2 LYS 1 46.250 30.800 25.850 1.00 0.00 \n+ATOM 13 CD LYS 1 47.340 31.790 27.300 1.00 0.00 \n+ATOM 14 HD1 LYS 1 48.120 32.060 26.590 1.00 0.00 \n+ATOM 15 HD2 LYS 1 47.240 32.680 27.910 1.00 0.00 \n+ATOM 16 CE LYS 1 47.650 30.530 28.100 1.00 0.00 \n+ATOM 17 HE1 LYS 1 46.940 30.360 28.920 1.00 0.00 \n+ATOM 18 HE2 LYS 1 47.660 29.700 27.400 1.00 0.00 \n+ATOM 19 NZ LYS 1 48.950 30.620 28.790 1.00 0.00 \n+ATOM 20 HZ1 LYS 1 48.940 29.910 29.510 1.00 0.00 \n+ATOM 21 HZ2 LYS 1 49.750 30.320 28.260 1.00 0.00 \n+ATOM 22 HZ3 LYS 1 49.130 31.520 29.220 1.00 0.00 \n+ATOM 23 C LYS 1 43.250 31.700 25.170 1.00 0.00 \n+ATOM 24 O LYS 1 42.260 32.360 25.490 1.00 0.00 \n+ATOM 25 N VAL 2 43.310 30.380 25.350 1.00 0.00 \n+ATOM 26 H VAL 2 44.200 29.980 25.100 1.00 0.00 \n+ATOM 27 CA VAL 2 42.400 29.530 26.090 1.00 0.00 \n+ATOM 28 HA VAL 2 41.600 30.100 26.570 1.00 0.00 \n+ATOM 29 CB VAL 2 41.810 28.480 25.150 1.00 0.00 \n+ATOM 30 HB VAL 2 42.530 27.670 24.980 1.00 0.00 \n+ATOM 31 CG1 VAL 2 40.650 27.800 25.880 1.00 0.00 \n+ATOM 32 1HG1 VAL 2 40.370 26.840 25.430 1.00 0.00 \n+ATOM 33 2HG1 VAL 2 40.850 27.580 26.930 1.00 0.00 \n+ATOM 34 3HG1 VAL 2 39.850 28.530 25.810 1.00 0.00 \n+ATOM 35 CG2 VAL 2 41.420 29.010 23.770 1.00 0.00 \n+ATOM 36 1HG2 VAL 2 40.770 28.440 23.110 1.00 0.00 \n+ATOM 37 2HG2 VAL 2 40.910 29.960 23.960 1.00 0.00 \n+ATOM 38 3HG2 VAL 2 42.370 29.110 23.250 1.00 0.00 \n+ATOM 39 C VAL 2 43.370 28.830 27.020 1.00 0.00 \n+ATOM 40 O VAL 2 44.230 28.050 26.600 1.00 0.00 \n+ATOM 41 N PHE 3 43.240 28.980 28.340 1.00 0.00 \n+ATOM 42 H PHE 3 42.470 29.560 28.660 1.00 0.00 \n+ATOM 43 CA PHE 3 44.070 28.260 29.280 1.00 0.00 \n+ATOM 44 HA PHE 3 45.130 28.210 29.030 1.00 0.00 \n+ATOM 45 CB PHE 3 43.970 28.990 30.610 1.00 0.00 \n+ATOM 46 HB1 PHE 3 42.940 29.260 30.820 1.00 0.00 \n+ATOM 47 HB2 PHE 3 44.040 28.360 31.500 1.00 0.00 \n+ATOM 48 CG PHE 3 44.970 30.110 30.810 1.00 0.0'..b'OW SOL 2252 58.890 68.740 62.970 1.00 0.00 \n+ATOM 38328 HW1 SOL 2252 59.110 67.890 63.450 1.00 0.00 \n+ATOM 38329 HW2 SOL 2252 58.720 68.550 62.010 1.00 0.00 \n+ATOM 38330 OW SOL 2253 62.630 69.480 71.830 1.00 0.00 \n+ATOM 38331 HW1 SOL 2253 62.680 69.580 70.840 1.00 0.00 \n+ATOM 38332 HW2 SOL 2253 61.740 69.810 72.160 1.00 0.00 \n+ATOM 38333 OW SOL 2254 0.870 56.750 67.430 1.00 0.00 \n+ATOM 38334 HW1 SOL 2254 0.860 56.620 66.440 1.00 0.00 \n+ATOM 38335 HW2 SOL 2254 1.420 57.560 67.650 1.00 0.00 \n+ATOM 38336 OW SOL 2255 59.820 59.660 59.900 1.00 0.00 \n+ATOM 38337 HW1 SOL 2255 60.640 59.440 59.360 1.00 0.00 \n+ATOM 38338 HW2 SOL 2255 59.500 58.830 60.370 1.00 0.00 \n+ATOM 38339 OW SOL 2256 59.200 59.310 66.810 1.00 0.00 \n+ATOM 38340 HW1 SOL 2256 58.610 58.590 66.460 1.00 0.00 \n+ATOM 38341 HW2 SOL 2256 59.120 60.120 66.240 1.00 0.00 \n+ATOM 38342 OW SOL 2257 64.740 71.760 61.270 1.00 0.00 \n+ATOM 38343 HW1 SOL 2257 64.220 71.880 60.420 1.00 0.00 \n+ATOM 38344 HW2 SOL 2257 64.160 71.330 61.960 1.00 0.00 \n+ATOM 38345 OW SOL 2258 70.410 58.320 66.010 1.00 0.00 \n+ATOM 38346 HW1 SOL 2258 70.310 57.440 66.470 1.00 0.00 \n+ATOM 38347 HW2 SOL 2258 70.440 59.050 66.700 1.00 0.00 \n+ATOM 38348 OW SOL 2259 68.010 55.450 64.920 1.00 0.00 \n+ATOM 38349 HW1 SOL 2259 67.740 54.490 64.800 1.00 0.00 \n+ATOM 38350 HW2 SOL 2259 68.690 55.510 65.650 1.00 0.00 \n+ATOM 38351 OW SOL 2260 64.270 67.760 58.860 1.00 0.00 \n+ATOM 38352 HW1 SOL 2260 64.080 66.840 59.190 1.00 0.00 \n+ATOM 38353 HW2 SOL 2260 65.260 67.920 58.860 1.00 0.00 \n+ATOM 38354 OW SOL 2261 64.860 71.690 67.610 1.00 0.00 \n+ATOM 38355 HW1 SOL 2261 65.380 72.300 68.210 1.00 0.00 \n+ATOM 38356 HW2 SOL 2261 65.490 71.070 67.140 1.00 0.00 \n+ATOM 38357 OW SOL 2262 68.970 55.630 59.660 1.00 0.00 \n+ATOM 38358 HW1 SOL 2262 68.570 55.450 58.760 1.00 0.00 \n+ATOM 38359 HW2 SOL 2262 68.610 56.480 60.020 1.00 0.00 \n+ATOM 38360 OW SOL 2263 67.340 60.860 62.390 1.00 0.00 \n+ATOM 38361 HW1 SOL 2263 66.370 60.610 62.330 1.00 0.00 \n+ATOM 38362 HW2 SOL 2263 67.650 60.760 63.340 1.00 0.00 \n+ATOM 38363 OW SOL 2264 72.570 57.230 64.750 1.00 0.00 \n+ATOM 38364 HW1 SOL 2264 72.000 57.840 65.310 1.00 0.00 \n+ATOM 38365 HW2 SOL 2264 72.180 57.170 63.830 1.00 0.00 \n+ATOM 38366 OW SOL 2265 56.360 64.300 57.960 1.00 0.00 \n+ATOM 38367 HW1 SOL 2265 57.050 64.960 58.220 1.00 0.00 \n+ATOM 38368 HW2 SOL 2265 56.170 63.690 58.730 1.00 0.00 \n+ATOM 38369 CL CL 2266 0.460 29.080 13.290 1.00 0.00 \n+ATOM 38370 CL CL 2267 15.130 24.050 31.780 1.00 0.00 \n+ATOM 38371 CL CL 2268 15.030 72.460 41.720 1.00 0.00 \n+ATOM 38372 CL CL 2269 15.230 63.640 57.410 1.00 0.00 \n+ATOM 38373 CL CL 2270 30.210 37.140 61.190 1.00 0.00 \n+ATOM 38374 CL CL 2271 27.560 41.050 16.730 1.00 0.00 \n+ATOM 38375 CL CL 2272 0.380 10.350 6.770 1.00 0.00 \n+ATOM 38376 CL CL 2273 62.610 56.750 57.100 1.00 0.00 \n+TER\n+ENDMDL\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/npt.tpr |
| b |
| Binary file test-data/npt.tpr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/npt.trr |
| b |
| Binary file test-data/npt.trr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/npt.xtc |
| b |
| Binary file test-data/npt.xtc has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/nvt.cpt |
| b |
| Binary file test-data/nvt.cpt has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/nvt.edr |
| b |
| Binary file test-data/nvt.edr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/nvt.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nvt.gro Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,38379 @@\n+LYSOZYME in water\n+38376\n+ 1LYS N 1 4.414 3.401 2.453 -0.1245 -0.0474 0.2586\n+ 1LYS H1 2 4.480 3.471 2.424 -1.7482 1.7484 0.6963\n+ 1LYS H2 3 4.360 3.369 2.373 1.2229 -3.2424 0.4578\n+ 1LYS H3 4 4.360 3.447 2.524 1.0582 -0.7342 1.6378\n+ 1LYS CA 5 4.470 3.280 2.516 -0.0047 -0.2324 -0.1924\n+ 1LYS HA 6 4.518 3.227 2.434 0.4015 -1.3689 0.7569\n+ 1LYS CB 7 4.571 3.318 2.624 0.0554 0.2713 -0.4193\n+ 1LYS HB1 8 4.656 3.370 2.579 1.2827 -2.2577 -1.2165\n+ 1LYS HB2 9 4.530 3.386 2.698 -2.5593 -0.6513 -0.9218\n+ 1LYS CG 10 4.629 3.200 2.703 -0.1547 0.7908 0.5244\n+ 1LYS HG1 11 4.555 3.152 2.767 0.2325 -0.6000 -0.0319\n+ 1LYS HG2 12 4.645 3.120 2.631 0.4708 -0.2729 1.7931\n+ 1LYS CD 13 4.756 3.218 2.787 -0.0525 -0.0302 0.5523\n+ 1LYS HD1 14 4.838 3.216 2.715 -1.1456 1.3793 -0.7946\n+ 1LYS HD2 15 4.755 3.307 2.850 -0.3160 0.0084 0.4945\n+ 1LYS CE 16 4.779 3.095 2.874 -0.2235 -0.7092 -0.3413\n+ 1LYS HE1 17 4.721 3.085 2.966 -0.4480 -0.6077 -0.4718\n+ 1LYS HE2 18 4.751 2.999 2.831 0.7916 -1.0155 -0.3551\n+ 1LYS NZ 19 4.918 3.074 2.917 -0.1350 0.6325 0.0733\n+ 1LYS HZ1 20 4.918 2.997 2.983 1.5256 1.2201 0.8122\n+ 1LYS HZ2 21 4.975 3.041 2.840 0.1468 -0.3915 0.6956\n+ 1LYS HZ3 22 4.965 3.152 2.960 -0.7788 -0.6938 3.5038\n+ 1LYS C 23 4.354 3.196 2.569 0.0087 -0.0224 0.1719\n+ 1LYS O 24 4.259 3.259 2.616 0.0177 0.0708 0.0670\n+ 2VAL N 25 4.363 3.063 2.561 -0.1064 -0.0118 -0.1221\n+ 2VAL H 26 4.434 3.024 2.501 -0.2930 1.8672 -1.6788\n+ 2VAL CA 27 4.283 2.971 2.638 0.4698 -0.4814 -0.0790\n+ 2VAL HA 28 4.216 3.027 2.703 0.9998 -0.9382 0.8779\n+ 2VAL CB 29 4.204 2.870 2.555 -0.1650 -0.1450 0.1125\n+ 2VAL HB 30 4.279 2.817 2.497 1.2857 0.2990 1.5321\n+ 2VAL CG1 31 4.124 2.766 2.633 -0.1354 -0.5454 -0.3815\n+ 2VAL HG11 32 4.107 2.674 2.577 -1.6514 -0.6805 0.2518\n+ 2VAL HG12 33 4.184 2.722 2.713 1.0901 -0.5350 -1.2752\n+ 2VAL HG13 34 4.034 2.810 2.677 0.0989 0.0960 -0.5416\n+ 2VAL CG2 35 4.119 2.939 2.448 0.4678 -0.5282 -0.6567\n+ 2VAL HG21 36 4.053 2.867 2.401 1.1537 -2.2692 0.9490\n+ 2VAL HG22 37 4.063 3.027 2.481 1.6915 -0.3405 1.0716\n+ 2VAL HG23 38 4.168 2.983 2.362 -1.4954 -0.9957 -2.0889\n+ 2VAL C 39 4.384 2.901 2.729 0.4193 -0.4889 -0.0284\n+ 2VAL O 40 4.466 2.823 2.682 0.7041 -0.3222 0.1888\n+ 3PHE N 41 4.373 2.931 2.858 0.0323 0.4997 -0.2799\n+ 3PHE H 42 4.291 2.987 2.879 -0.1551 0.5609 -1.1538\n+ 3PHE CA 43 4.441 2.860 2.964 0.0286 0.0987 -0.5454\n+ 3PHE HA 44 4.547 2.852 2.942 0.2612 1.2032 0.0765\n+ 3PHE CB 45 4.429 2.933 3.098 0.0231 -0.2686 -0.3451\n+ 3PHE HB1 46 4.325 2.964 3.109 0.1691 0.3214 -0.6368\n+ 3PHE HB2 47 4.456 2.861 3.176 -2.9863 -1.9433 -0.7003\n+ 3PHE CG 48 4.516 3.054 3.120 -0.5309 0.1005 -0.1759\n+ 3PHE CD1 49 4.485 3.179 3.065 0.0236 0.2578 -0.1378\n+ 3PHE HD1 50 4.394 3.183 3.007 0.5847 2.0394 -0.9705\n+ 3PHE CD2 51 4.629 3.045 3.203 -0.3055 0.2147 -0.4689\n+ 3PHE HD2 52 4.649 2.948 3.247 -1.8630 -0.0414 -0.2471\n+ 3PHE CE1 53 4.566 3.291 3.085 -0.2488 0.3937 0.2120\n+ 3PHE HE1 54 4.552 3.385 3.034 -0.8507 -0.5038 -1.3251\n+ 3PHE CE2 55 4.709 3.156 3.231 0.1445 -0.2260 0.0278\n+ 3PHE HE2 56 4.797 3.155 3.293 0.2985 -0.2584 -0.1904\n+ 3PHE CZ 57 4.670 3'..b' 6.425 6.613 6.599 -1.0242 0.2185 -1.3474\n+12250SOL OW38321 6.657 6.605 5.680 0.3901 0.0131 -0.3337\n+12250SOL HW138322 6.633 6.659 5.599 1.3684 0.2384 -0.4807\n+12250SOL HW238323 6.689 6.515 5.651 0.0465 -0.1673 -0.1570\n+12251SOL OW38324 0.130 7.022 6.323 -0.6970 0.3793 0.3726\n+12251SOL HW138325 0.070 7.025 6.243 -0.5860 0.7074 0.3000\n+12251SOL HW238326 0.081 6.983 6.400 -0.8316 0.1371 0.1664\n+12252SOL OW38327 5.803 7.014 6.256 0.8681 0.1038 -0.4046\n+12252SOL HW138328 5.739 7.004 6.332 1.4817 2.5250 0.5358\n+12252SOL HW238329 5.868 6.938 6.255 0.0248 -0.6408 0.6669\n+12253SOL OW38330 6.328 6.949 0.001 0.1972 0.4320 -0.2740\n+12253SOL HW138331 6.262 7.005 -0.049 -1.8563 -0.9533 0.7621\n+12253SOL HW238332 6.312 6.958 0.100 -1.3131 -3.0889 -0.0559\n+12254SOL OW38333 7.300 5.683 6.714 0.4791 -0.6901 -0.2548\n+12254SOL HW138334 7.211 5.637 6.709 0.1350 -0.1306 0.5088\n+12254SOL HW238335 7.310 5.744 6.635 0.8833 -1.9321 -1.2090\n+12255SOL OW38336 5.959 5.962 6.015 0.3415 0.1915 -0.3612\n+12255SOL HW138337 6.057 5.982 6.022 0.0066 2.3032 -0.9173\n+12255SOL HW238338 5.923 5.941 6.106 1.0001 1.1962 0.1594\n+12256SOL OW38339 6.082 6.039 6.890 0.3357 0.1814 0.2938\n+12256SOL HW138340 6.112 5.960 6.943 0.7081 0.3525 0.3422\n+12256SOL HW238341 6.026 6.008 6.813 0.8614 -0.1696 0.0454\n+12257SOL OW38342 6.349 7.297 6.285 0.1509 -0.5373 -0.1490\n+12257SOL HW138343 6.338 7.324 6.189 0.8201 -0.5969 -0.2474\n+12257SOL HW238344 6.288 7.220 6.305 -0.5064 -0.0704 -0.3306\n+12258SOL OW38345 6.993 5.869 6.615 -0.1606 -0.6358 0.1122\n+12258SOL HW138346 6.986 5.770 6.630 1.9995 -0.6580 1.3854\n+12258SOL HW238347 6.994 5.916 6.704 -0.2335 0.4563 -0.4484\n+12259SOL OW38348 6.768 5.570 6.534 0.2539 -0.6929 0.0861\n+12259SOL HW138349 6.758 5.472 6.518 -0.2914 -0.6407 0.1076\n+12259SOL HW238350 6.843 5.585 6.599 0.1145 -1.1156 0.3492\n+12260SOL OW38351 6.399 6.980 6.060 -0.1377 0.1280 -0.0719\n+12260SOL HW138352 6.409 6.882 6.071 0.6528 0.1708 -0.3591\n+12260SOL HW238353 6.445 7.028 6.135 0.0790 0.2873 -0.3029\n+12261SOL OW38354 6.415 7.221 6.854 -0.0785 0.1304 -0.0085\n+12261SOL HW138355 6.445 7.304 6.902 -1.3458 -0.3725 1.7852\n+12261SOL HW238356 6.494 7.162 6.837 0.8138 1.5874 -1.1435\n+12262SOL OW38357 7.079 5.424 5.840 -0.0092 -0.0703 0.6338\n+12262SOL HW138358 7.075 5.331 5.803 -0.8219 0.6173 -1.1521\n+12262SOL HW238359 6.986 5.460 5.849 0.3300 0.9183 0.3329\n+12263SOL OW38360 6.774 6.147 6.184 0.2869 -0.0267 -0.0207\n+12263SOL HW138361 6.679 6.119 6.173 0.5632 -0.7216 -0.8357\n+12263SOL HW238362 6.818 6.089 6.253 0.6721 -1.2110 -1.2034\n+12264SOL OW38363 7.235 5.877 6.502 -0.2037 0.0926 0.5223\n+12264SOL HW138364 7.143 5.880 6.541 -0.2123 -0.7042 0.5772\n+12264SOL HW238365 7.229 5.862 6.403 -0.1222 -0.8795 0.6546\n+12265SOL OW38366 5.757 6.516 5.839 -0.2663 -0.5555 -0.4616\n+12265SOL HW138367 5.852 6.543 5.827 -1.1659 3.7337 0.6551\n+12265SOL HW238368 5.739 6.501 5.936 -0.8181 -1.1802 -0.6528\n+12266CL CL38369 0.011 2.983 1.283 0.0958 0.7921 0.1589\n+12267CL CL38370 1.624 2.346 3.356 -0.4632 -0.0375 0.0503\n+12268CL CL38371 1.563 7.224 4.160 -0.2199 0.1409 -0.2564\n+12269CL CL38372 1.475 6.421 5.828 -0.0800 -0.2095 0.2597\n+12270CL CL38373 3.128 3.790 6.172 -0.1431 0.0850 0.4640\n+12271CL CL38374 2.774 4.120 1.873 -0.2138 -0.2134 -0.0755\n+12272CL CL38375 7.334 1.044 0.689 0.3876 0.0282 0.0509\n+12273CL CL38376 6.342 5.664 5.947 0.1102 0.1942 0.1584\n+ 7.33925 7.33925 7.33925\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/nvt.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nvt.mdp Thu Oct 04 17:38:27 2018 -0400 |
| b |
| @@ -0,0 +1,43 @@ +title = OPLS Lysozyme NVT equilibration +define = -DPOSRES ; position restrain the protein +; Run parameters +integrator = md ; leap-frog integrator +nsteps = 500 ; 2 * 50000 = 100 ps +dt = 0.002 ; 2 fs +; Output control +nstxout = 50 ; save coordinates every 1.0 ps +nstvout = 50 ; save velocities every 1.0 ps +nstenergy = 50 ; save energies every 1.0 ps +nstlog = 50 ; update log file every 1.0 ps +nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps +; Bond parameters +continuation = no ; first dynamics run +constraint_algorithm = lincs ; holonomic constraints +constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained +lincs_iter = 1 ; accuracy of LINCS +lincs_order = 4 ; also related to accuracy +; Neighborsearching +cutoff-scheme = Verlet +ns_type = grid ; search neighboring grid cells +nstlist = 10 ; 20 fs, largely irrelevant with Verlet +rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) +rvdw = 1.0 ; short-range van der Waals cutoff (in nm) +; Electrostatics +coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics +pme_order = 4 ; cubic interpolation +fourierspacing = 0.16 ; grid spacing for FFT +; Temperature coupling is on +tcoupl = V-rescale ; modified Berendsen thermostat +tc-grps = Protein Non-Protein ; two coupling groups - more accurate +tau_t = 0.1 0.1 ; time constant, in ps +ref_t = 300 300 ; reference temperature, one for each group, in K +; Pressure coupling is off +pcoupl = no ; no pressure coupling in NVT +; Periodic boundary conditions +pbc = xyz ; 3-D PBC +; Dispersion correction +DispCorr = EnerPres ; account for cut-off vdW scheme +; Velocity generation +gen_vel = yes ; assign velocities from Maxwell distribution +gen_temp = 300 ; temperature for Maxwell distribution +gen_seed = -1 ; generate a random seed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/nvt.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nvt.pdb Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,38382 @@\n+TITLE LYSOZYME in water\n+REMARK THIS IS A SIMULATION BOX\n+CRYST1 73.393 73.393 73.393 90.00 90.00 90.00 P 1 1\n+MODEL 1\n+ATOM 1 N LYS 1 44.140 34.010 24.530 1.00 0.00 \n+ATOM 2 H1 LYS 1 44.800 34.710 24.240 1.00 0.00 \n+ATOM 3 H2 LYS 1 43.600 33.690 23.730 1.00 0.00 \n+ATOM 4 H3 LYS 1 43.600 34.470 25.240 1.00 0.00 \n+ATOM 5 CA LYS 1 44.700 32.800 25.160 1.00 0.00 \n+ATOM 6 HA LYS 1 45.180 32.270 24.340 1.00 0.00 \n+ATOM 7 CB LYS 1 45.710 33.180 26.240 1.00 0.00 \n+ATOM 8 HB1 LYS 1 46.560 33.700 25.790 1.00 0.00 \n+ATOM 9 HB2 LYS 1 45.300 33.860 26.980 1.00 0.00 \n+ATOM 10 CG LYS 1 46.290 32.000 27.030 1.00 0.00 \n+ATOM 11 HG1 LYS 1 45.550 31.520 27.670 1.00 0.00 \n+ATOM 12 HG2 LYS 1 46.450 31.200 26.310 1.00 0.00 \n+ATOM 13 CD LYS 1 47.560 32.180 27.870 1.00 0.00 \n+ATOM 14 HD1 LYS 1 48.380 32.160 27.150 1.00 0.00 \n+ATOM 15 HD2 LYS 1 47.550 33.070 28.500 1.00 0.00 \n+ATOM 16 CE LYS 1 47.790 30.950 28.740 1.00 0.00 \n+ATOM 17 HE1 LYS 1 47.210 30.850 29.660 1.00 0.00 \n+ATOM 18 HE2 LYS 1 47.510 29.990 28.310 1.00 0.00 \n+ATOM 19 NZ LYS 1 49.180 30.740 29.170 1.00 0.00 \n+ATOM 20 HZ1 LYS 1 49.180 29.970 29.830 1.00 0.00 \n+ATOM 21 HZ2 LYS 1 49.750 30.410 28.400 1.00 0.00 \n+ATOM 22 HZ3 LYS 1 49.650 31.520 29.600 1.00 0.00 \n+ATOM 23 C LYS 1 43.540 31.960 25.690 1.00 0.00 \n+ATOM 24 O LYS 1 42.590 32.590 26.160 1.00 0.00 \n+ATOM 25 N VAL 2 43.630 30.630 25.610 1.00 0.00 \n+ATOM 26 H VAL 2 44.340 30.240 25.010 1.00 0.00 \n+ATOM 27 CA VAL 2 42.830 29.710 26.380 1.00 0.00 \n+ATOM 28 HA VAL 2 42.160 30.270 27.030 1.00 0.00 \n+ATOM 29 CB VAL 2 42.040 28.700 25.550 1.00 0.00 \n+ATOM 30 HB VAL 2 42.790 28.170 24.970 1.00 0.00 \n+ATOM 31 CG1 VAL 2 41.240 27.660 26.330 1.00 0.00 \n+ATOM 32 1HG1 VAL 2 41.070 26.740 25.770 1.00 0.00 \n+ATOM 33 2HG1 VAL 2 41.840 27.220 27.130 1.00 0.00 \n+ATOM 34 3HG1 VAL 2 40.340 28.100 26.770 1.00 0.00 \n+ATOM 35 CG2 VAL 2 41.190 29.390 24.480 1.00 0.00 \n+ATOM 36 1HG2 VAL 2 40.530 28.670 24.010 1.00 0.00 \n+ATOM 37 2HG2 VAL 2 40.630 30.270 24.810 1.00 0.00 \n+ATOM 38 3HG2 VAL 2 41.680 29.830 23.620 1.00 0.00 \n+ATOM 39 C VAL 2 43.840 29.010 27.290 1.00 0.00 \n+ATOM 40 O VAL 2 44.660 28.230 26.820 1.00 0.00 \n+ATOM 41 N PHE 3 43.730 29.310 28.580 1.00 0.00 \n+ATOM 42 H PHE 3 42.910 29.870 28.790 1.00 0.00 \n+ATOM 43 CA PHE 3 44.410 28.600 29.640 1.00 0.00 \n+ATOM 44 HA PHE 3 45.470 28.520 29.420 1.00 0.00 \n+ATOM 45 CB PHE 3 44.290 29.330 30.980 1.00 0.00 \n+ATOM 46 HB1 PHE 3 43.250 29.640 31.090 1.00 0.00 \n+ATOM 47 HB2 PHE 3 44.560 28.610 31.760 1.00 0.00 \n+ATOM 48 CG PHE 3 45.160 30.540 31.200 1.00 0.0'..b'OW SOL 2252 58.030 70.140 62.560 1.00 0.00 \n+ATOM 38328 HW1 SOL 2252 57.390 70.040 63.320 1.00 0.00 \n+ATOM 38329 HW2 SOL 2252 58.680 69.380 62.550 1.00 0.00 \n+ATOM 38330 OW SOL 2253 63.280 69.490 0.010 1.00 0.00 \n+ATOM 38331 HW1 SOL 2253 62.620 70.050 -0.490 1.00 0.00 \n+ATOM 38332 HW2 SOL 2253 63.120 69.580 1.000 1.00 0.00 \n+ATOM 38333 OW SOL 2254 73.000 56.830 67.140 1.00 0.00 \n+ATOM 38334 HW1 SOL 2254 72.110 56.370 67.090 1.00 0.00 \n+ATOM 38335 HW2 SOL 2254 73.100 57.440 66.350 1.00 0.00 \n+ATOM 38336 OW SOL 2255 59.590 59.620 60.150 1.00 0.00 \n+ATOM 38337 HW1 SOL 2255 60.570 59.820 60.220 1.00 0.00 \n+ATOM 38338 HW2 SOL 2255 59.230 59.410 61.060 1.00 0.00 \n+ATOM 38339 OW SOL 2256 60.820 60.390 68.900 1.00 0.00 \n+ATOM 38340 HW1 SOL 2256 61.120 59.600 69.430 1.00 0.00 \n+ATOM 38341 HW2 SOL 2256 60.260 60.080 68.130 1.00 0.00 \n+ATOM 38342 OW SOL 2257 63.490 72.970 62.850 1.00 0.00 \n+ATOM 38343 HW1 SOL 2257 63.380 73.240 61.890 1.00 0.00 \n+ATOM 38344 HW2 SOL 2257 62.880 72.200 63.050 1.00 0.00 \n+ATOM 38345 OW SOL 2258 69.930 58.690 66.150 1.00 0.00 \n+ATOM 38346 HW1 SOL 2258 69.860 57.700 66.300 1.00 0.00 \n+ATOM 38347 HW2 SOL 2258 69.940 59.160 67.040 1.00 0.00 \n+ATOM 38348 OW SOL 2259 67.680 55.700 65.340 1.00 0.00 \n+ATOM 38349 HW1 SOL 2259 67.580 54.720 65.180 1.00 0.00 \n+ATOM 38350 HW2 SOL 2259 68.430 55.850 65.990 1.00 0.00 \n+ATOM 38351 OW SOL 2260 63.990 69.800 60.600 1.00 0.00 \n+ATOM 38352 HW1 SOL 2260 64.090 68.820 60.710 1.00 0.00 \n+ATOM 38353 HW2 SOL 2260 64.450 70.280 61.350 1.00 0.00 \n+ATOM 38354 OW SOL 2261 64.150 72.210 68.540 1.00 0.00 \n+ATOM 38355 HW1 SOL 2261 64.450 73.040 69.020 1.00 0.00 \n+ATOM 38356 HW2 SOL 2261 64.940 71.620 68.370 1.00 0.00 \n+ATOM 38357 OW SOL 2262 70.790 54.240 58.400 1.00 0.00 \n+ATOM 38358 HW1 SOL 2262 70.750 53.310 58.030 1.00 0.00 \n+ATOM 38359 HW2 SOL 2262 69.860 54.600 58.490 1.00 0.00 \n+ATOM 38360 OW SOL 2263 67.740 61.470 61.840 1.00 0.00 \n+ATOM 38361 HW1 SOL 2263 66.790 61.190 61.730 1.00 0.00 \n+ATOM 38362 HW2 SOL 2263 68.180 60.890 62.530 1.00 0.00 \n+ATOM 38363 OW SOL 2264 72.350 58.770 65.020 1.00 0.00 \n+ATOM 38364 HW1 SOL 2264 71.430 58.800 65.410 1.00 0.00 \n+ATOM 38365 HW2 SOL 2264 72.290 58.620 64.030 1.00 0.00 \n+ATOM 38366 OW SOL 2265 57.570 65.160 58.390 1.00 0.00 \n+ATOM 38367 HW1 SOL 2265 58.520 65.430 58.270 1.00 0.00 \n+ATOM 38368 HW2 SOL 2265 57.390 65.010 59.360 1.00 0.00 \n+ATOM 38369 CL CL 2266 0.110 29.830 12.830 1.00 0.00 \n+ATOM 38370 CL CL 2267 16.240 23.460 33.560 1.00 0.00 \n+ATOM 38371 CL CL 2268 15.630 72.240 41.600 1.00 0.00 \n+ATOM 38372 CL CL 2269 14.750 64.210 58.280 1.00 0.00 \n+ATOM 38373 CL CL 2270 31.280 37.900 61.720 1.00 0.00 \n+ATOM 38374 CL CL 2271 27.740 41.200 18.730 1.00 0.00 \n+ATOM 38375 CL CL 2272 73.340 10.440 6.890 1.00 0.00 \n+ATOM 38376 CL CL 2273 63.420 56.640 59.470 1.00 0.00 \n+TER\n+ENDMDL\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/nvt.tpr |
| b |
| Binary file test-data/nvt.tpr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/nvt.trr |
| b |
| Binary file test-data/nvt.trr has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/nvt.xtc |
| b |
| Binary file test-data/nvt.xtc has changed |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/posres.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posres.itp Thu Oct 04 17:38:27 2018 -0400 |
| [ |
| b'@@ -0,0 +1,1008 @@\n+; In this topology include file, you will find position restraint\n+; entries for all the heavy atoms in your original pdb file.\n+; This means that all the protons which were added by pdb2gmx are\n+; not restrained.\n+\n+[ position_restraints ]\n+; atom type fx fy fz\n+ 1 1 1000 1000 1000\n+ 5 1 1000 1000 1000\n+ 7 1 1000 1000 1000\n+ 10 1 1000 1000 1000\n+ 13 1 1000 1000 1000\n+ 16 1 1000 1000 1000\n+ 19 1 1000 1000 1000\n+ 23 1 1000 1000 1000\n+ 24 1 1000 1000 1000\n+ 25 1 1000 1000 1000\n+ 27 1 1000 1000 1000\n+ 29 1 1000 1000 1000\n+ 31 1 1000 1000 1000\n+ 35 1 1000 1000 1000\n+ 39 1 1000 1000 1000\n+ 40 1 1000 1000 1000\n+ 41 1 1000 1000 1000\n+ 43 1 1000 1000 1000\n+ 45 1 1000 1000 1000\n+ 48 1 1000 1000 1000\n+ 49 1 1000 1000 1000\n+ 51 1 1000 1000 1000\n+ 53 1 1000 1000 1000\n+ 55 1 1000 1000 1000\n+ 57 1 1000 1000 1000\n+ 59 1 1000 1000 1000\n+ 60 1 1000 1000 1000\n+ 61 1 1000 1000 1000\n+ 63 1 1000 1000 1000\n+ 66 1 1000 1000 1000\n+ 67 1 1000 1000 1000\n+ 68 1 1000 1000 1000\n+ 70 1 1000 1000 1000\n+ 72 1 1000 1000 1000\n+ 75 1 1000 1000 1000\n+ 78 1 1000 1000 1000\n+ 81 1 1000 1000 1000\n+ 83 1 1000 1000 1000\n+ 84 1 1000 1000 1000\n+ 87 1 1000 1000 1000\n+ 90 1 1000 1000 1000\n+ 91 1 1000 1000 1000\n+ 92 1 1000 1000 1000\n+ 94 1 1000 1000 1000\n+ 96 1 1000 1000 1000\n+ 99 1 1000 1000 1000\n+ 100 1 1000 1000 1000\n+ 101 1 1000 1000 1000\n+ 102 1 1000 1000 1000\n+ 104 1 1000 1000 1000\n+ 106 1 1000 1000 1000\n+ 109 1 1000 1000 1000\n+ 112 1 1000 1000 1000\n+ 113 1 1000 1000 1000\n+ 114 1 1000 1000 1000\n+ 115 1 1000 1000 1000\n+ 116 1 1000 1000 1000\n+ 117 1 1000 1000 1000\n+ 119 1 1000 1000 1000\n+ 121 1 1000 1000 1000\n+ 124 1 1000 1000 1000\n+ 126 1 1000 1000 1000\n+ 130 1 1000 1000 1000\n+ 134 1 1000 1000 1000\n+ 135 1 1000 1000 1000\n+ 136 1 1000 1000 1000\n+ 138 1 1000 1000 1000\n+ 140 1 1000 1000 1000\n+ 144 1 1000 1000 1000\n+ 145 1 1000 1000 1000\n+ 146 1 1000 1000 1000\n+ 148 1 1000 1000 1000\n+ 150 1 1000 1000 1000\n+ 154 1 1000 1000 1000\n+ 155 1 1000 1000 1000\n+ 156 1 1000 1000 1000\n+ 158 1 1000 1000 1000\n+ 160 1 1000 1000 1000\n+ 164 1 1000 1000 1000\n+ 165 1 1000 1000 1000\n+ 166 1 1000 1000 1000\n+ 168 1 1000 1000 1000\n+ 170 1 1000 1000 1000\n+ 173 1 1000 1000 1000\n+ 176 1 1000 1000 1000\n+ 177 1 1000 1000 1000\n+ 181 1 1000 1000 1000\n+ 182 1 1000 1000 1000\n+ 183 1 1000 1000 1000\n+ 185 1 1000 1000 1000\n+ 187 1 1000 1000 1000\n+ 190 1 1000 1000 1000\n+ 193 1 1000 1000 1000\n+ 196 1 1000 1000 1000\n+ 199 1 1000 1000 1000\n+ 203 1 1000 1000 1000\n+ 204 1 1000 1000 1000\n+ 205 1 1000 1000 1000\n+ 207 1 1000 1000 1000\n+ 209 1 1000 1000 1000\n+ 212 1 1000 1000 1000\n+ 215 1 1000 1000 1000\n+ 218 1 1000 1000 1000\n+ 220 1 1000 1000 1000\n+ 221 1 1000 1000 1000\n+ 224 1 1000 1000 1000\n+ 227 1 1000 1000 1000\n+ 228 1 1000 1000 1000\n+ 229 1 1000 1000 1000\n+ 231 1 1000 1000 1000\n+ 233 1 1000 1000 1000\n+ 236 1 1000 1000 1000\n+ 237 1 1000 1000 1000\n+ 238 1 1000 1000 1000\n+ 240 1 1000 1000 1000\n+ 242 1 1000 '..b' 1711 1 1000 1000 1000\n+ 1714 1 1000 1000 1000\n+ 1716 1 1000 1000 1000\n+ 1717 1 1000 1000 1000\n+ 1720 1 1000 1000 1000\n+ 1723 1 1000 1000 1000\n+ 1724 1 1000 1000 1000\n+ 1725 1 1000 1000 1000\n+ 1727 1 1000 1000 1000\n+ 1729 1 1000 1000 1000\n+ 1732 1 1000 1000 1000\n+ 1733 1 1000 1000 1000\n+ 1734 1 1000 1000 1000\n+ 1735 1 1000 1000 1000\n+ 1737 1 1000 1000 1000\n+ 1739 1 1000 1000 1000\n+ 1742 1 1000 1000 1000\n+ 1745 1 1000 1000 1000\n+ 1748 1 1000 1000 1000\n+ 1751 1 1000 1000 1000\n+ 1755 1 1000 1000 1000\n+ 1756 1 1000 1000 1000\n+ 1757 1 1000 1000 1000\n+ 1759 1 1000 1000 1000\n+ 1762 1 1000 1000 1000\n+ 1763 1 1000 1000 1000\n+ 1764 1 1000 1000 1000\n+ 1766 1 1000 1000 1000\n+ 1768 1 1000 1000 1000\n+ 1770 1 1000 1000 1000\n+ 1772 1 1000 1000 1000\n+ 1776 1 1000 1000 1000\n+ 1777 1 1000 1000 1000\n+ 1778 1 1000 1000 1000\n+ 1780 1 1000 1000 1000\n+ 1782 1 1000 1000 1000\n+ 1785 1 1000 1000 1000\n+ 1786 1 1000 1000 1000\n+ 1787 1 1000 1000 1000\n+ 1788 1 1000 1000 1000\n+ 1789 1 1000 1000 1000\n+ 1790 1 1000 1000 1000\n+ 1792 1 1000 1000 1000\n+ 1794 1 1000 1000 1000\n+ 1796 1 1000 1000 1000\n+ 1800 1 1000 1000 1000\n+ 1804 1 1000 1000 1000\n+ 1805 1 1000 1000 1000\n+ 1806 1 1000 1000 1000\n+ 1808 1 1000 1000 1000\n+ 1810 1 1000 1000 1000\n+ 1813 1 1000 1000 1000\n+ 1816 1 1000 1000 1000\n+ 1817 1 1000 1000 1000\n+ 1818 1 1000 1000 1000\n+ 1821 1 1000 1000 1000\n+ 1822 1 1000 1000 1000\n+ 1823 1 1000 1000 1000\n+ 1825 1 1000 1000 1000\n+ 1827 1 1000 1000 1000\n+ 1831 1 1000 1000 1000\n+ 1832 1 1000 1000 1000\n+ 1833 1 1000 1000 1000\n+ 1835 1 1000 1000 1000\n+ 1837 1 1000 1000 1000\n+ 1840 1 1000 1000 1000\n+ 1841 1 1000 1000 1000\n+ 1843 1 1000 1000 1000\n+ 1844 1 1000 1000 1000\n+ 1846 1 1000 1000 1000\n+ 1847 1 1000 1000 1000\n+ 1849 1 1000 1000 1000\n+ 1851 1 1000 1000 1000\n+ 1853 1 1000 1000 1000\n+ 1855 1 1000 1000 1000\n+ 1856 1 1000 1000 1000\n+ 1857 1 1000 1000 1000\n+ 1859 1 1000 1000 1000\n+ 1861 1 1000 1000 1000\n+ 1863 1 1000 1000 1000\n+ 1866 1 1000 1000 1000\n+ 1870 1 1000 1000 1000\n+ 1874 1 1000 1000 1000\n+ 1875 1 1000 1000 1000\n+ 1876 1 1000 1000 1000\n+ 1878 1 1000 1000 1000\n+ 1880 1 1000 1000 1000\n+ 1883 1 1000 1000 1000\n+ 1886 1 1000 1000 1000\n+ 1889 1 1000 1000 1000\n+ 1891 1 1000 1000 1000\n+ 1892 1 1000 1000 1000\n+ 1895 1 1000 1000 1000\n+ 1898 1 1000 1000 1000\n+ 1899 1 1000 1000 1000\n+ 1900 1 1000 1000 1000\n+ 1902 1 1000 1000 1000\n+ 1905 1 1000 1000 1000\n+ 1906 1 1000 1000 1000\n+ 1907 1 1000 1000 1000\n+ 1909 1 1000 1000 1000\n+ 1911 1 1000 1000 1000\n+ 1914 1 1000 1000 1000\n+ 1915 1 1000 1000 1000\n+ 1916 1 1000 1000 1000\n+ 1917 1 1000 1000 1000\n+ 1919 1 1000 1000 1000\n+ 1921 1 1000 1000 1000\n+ 1924 1 1000 1000 1000\n+ 1927 1 1000 1000 1000\n+ 1930 1 1000 1000 1000\n+ 1932 1 1000 1000 1000\n+ 1933 1 1000 1000 1000\n+ 1936 1 1000 1000 1000\n+ 1939 1 1000 1000 1000\n+ 1940 1 1000 1000 1000\n+ 1941 1 1000 1000 1000\n+ 1943 1 1000 1000 1000\n+ 1945 1 1000 1000 1000\n+ 1948 1 1000 1000 1000\n+ 1950 1 1000 1000 1000\n+ 1954 1 1000 1000 1000\n+ 1958 1 1000 1000 1000\n+ 1959 1 1000 1000 1000\n+ 1960 1 1000 1000 1000\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/processed.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/processed.gro Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,2197 @@\n+LYSOZYME\n+ 2194\n+ 1LYS N 1 3.536 2.234 -1.198\n+ 1LYS H1 2 3.612 2.288 -1.236\n+ 1LYS H2 3 3.470 2.214 -1.270\n+ 1LYS H3 4 3.492 2.286 -1.125\n+ 1LYS CA 5 3.589 2.107 -1.143\n+ 1LYS HA 6 3.633 2.055 -1.216\n+ 1LYS CB 7 3.687 2.144 -1.031\n+ 1LYS HB1 8 3.763 2.195 -1.070\n+ 1LYS HB2 9 3.639 2.201 -0.964\n+ 1LYS CG 10 3.745 2.025 -0.956\n+ 1LYS HG1 11 3.676 1.989 -0.894\n+ 1LYS HG2 12 3.770 1.954 -1.023\n+ 1LYS CD 13 3.869 2.065 -0.877\n+ 1LYS HD1 14 3.945 2.083 -0.940\n+ 1LYS HD2 15 3.849 2.147 -0.824\n+ 1LYS CE 16 3.906 1.951 -0.784\n+ 1LYS HE1 17 3.841 1.946 -0.708\n+ 1LYS HE2 18 3.906 1.864 -0.833\n+ 1LYS NZ 19 4.042 1.977 -0.730\n+ 1LYS HZ1 20 4.069 1.903 -0.668\n+ 1LYS HZ2 21 4.108 1.982 -0.806\n+ 1LYS HZ3 22 4.042 2.064 -0.680\n+ 1LYS C 23 3.474 2.026 -1.084\n+ 1LYS O 24 3.395 2.081 -1.008\n+ 2VAL N 25 3.474 1.896 -1.104\n+ 2VAL H 26 3.536 1.860 -1.174\n+ 2VAL CA 27 3.390 1.800 -1.033\n+ 2VAL HA 28 3.317 1.852 -0.990\n+ 2VAL CB 29 3.314 1.703 -1.123\n+ 2VAL HB 30 3.386 1.652 -1.170\n+ 2VAL CG1 31 3.225 1.608 -1.043\n+ 2VAL HG11 32 3.177 1.547 -1.106\n+ 2VAL HG12 33 3.282 1.555 -0.981\n+ 2VAL HG13 34 3.158 1.661 -0.991\n+ 2VAL CG2 35 3.229 1.771 -1.229\n+ 2VAL HG21 36 3.183 1.702 -1.284\n+ 2VAL HG22 37 3.162 1.830 -1.185\n+ 2VAL HG23 38 3.288 1.827 -1.288\n+ 2VAL C 39 3.480 1.731 -0.929\n+ 2VAL O 40 3.576 1.661 -0.966\n+ 3PHE N 41 3.449 1.755 -0.804\n+ 3PHE H 42 3.375 1.819 -0.784\n+ 3PHE CA 43 3.519 1.690 -0.692\n+ 3PHE HA 44 3.615 1.697 -0.717\n+ 3PHE CB 45 3.497 1.763 -0.559\n+ 3PHE HB1 46 3.405 1.802 -0.558\n+ 3PHE HB2 47 3.506 1.698 -0.484\n+ 3PHE CG 48 3.594 1.874 -0.538\n+ 3PHE CD1 49 3.567 2.005 -0.580\n+ 3PHE HD1 50 3.481 2.025 -0.627\n+ 3PHE CD2 51 3.700 1.856 -0.447\n+ 3PHE HD2 52 3.713 1.766 -0.405\n+ 3PHE CE1 53 3.658 2.108 -0.557\n+ 3PHE HE1 54 3.648 2.195 -0.604\n+ 3PHE CE2 55 3.787 1.959 -0.416\n+ 3PHE HE2 56 3.866 1.942 -0.357\n+ 3PHE CZ 57 3.764 2.087 -0.467\n+ 3PHE HZ 58 3.822 2.164 -0.439\n+ 3PHE C 59 3.474 1.544 -0.677\n+ 3PHE O 60 3.352 1.516 -0.686\n+ 4GLY N 61 3.572 1.464 -0.633\n+ 4GLY H 62 3.667 1.495 -0.632\n+ 4GLY CA 63 3.537 1.328 -0.587\n+ 4GLY HA1 64 3.462 1.292 -0.643\n+ 4GLY HA2 65 3.616 1.268 -0.594\n+ 4GLY C 66 3.492 1.342 -0.442\n+ 4GLY O 67 3.530 1.440 -0.378\n+ 5ARG N 68 3.405 1.254 -0.397\n+ 5ARG H 69 3.371 1.184 -0.460\n+ 5ARG CA 70 3.356 1.254 -0.259\n+ 5ARG HA 71 3.298 1.334 -0.252\n+ 5ARG CB 72 3.276 1.126 -0.233\n+ 5ARG HB1 73 3.200 1.122 -0.297\n+ 5ARG HB2 74 3.336 1.047 -0.247\n+ 5ARG CG 75 3.221 1.120 -0.092\n+ 5ARG HG1 76 3.297 1.117 -0.027\n+ 5ARG HG2 77 3.165 1.201 -0.075\n+ 5ARG CD 78 3.138 1.000 -0.072\n+ 5ARG HD1 79 3.104 0.999 0.022\n+ 5ARG HD2 80 3.060 1.005 -0.135\n+ 5ARG NE 81 3.206 0.875 -0.096\n+ 5ARG HE 82 3.202 0.840 -0.189\n+ 5ARG CZ 83 3.273 0.801 -0.010\n+ 5ARG NH1 84 3.284 0.833 0.119\n+ 5ARG HH11 85 3.239 0.916 0.153\n+ 5ARG HH12 86 3.336 0.775 0.181\n+ 5A'..b'81 1.000\n+ 179HOH HW1 2109 2.306 1.581 1.058\n+ 179HOH HW2 2110 2.224 1.663 0.942\n+ 180HOH OW 2111 4.073 0.922 0.029\n+ 180HOH HW1 2112 4.155 0.922 0.087\n+ 180HOH HW2 2113 4.073 0.841 -0.029\n+ 181HOH OW 2114 1.250 1.527 0.410\n+ 181HOH HW1 2115 1.168 1.527 0.467\n+ 181HOH HW2 2116 1.250 1.608 0.352\n+ 182HOH OW 2117 2.037 2.862 -0.235\n+ 182HOH HW1 2118 1.956 2.862 -0.178\n+ 182HOH HW2 2119 2.037 2.780 -0.293\n+ 183HOH OW 2120 2.279 1.546 -0.667\n+ 183HOH HW1 2121 2.279 1.628 -0.725\n+ 183HOH HW2 2122 2.279 1.465 -0.725\n+ 184HOH OW 2123 2.314 3.181 1.512\n+ 184HOH HW1 2124 2.395 3.181 1.570\n+ 184HOH HW2 2125 2.232 3.181 1.570\n+ 185HOH OW 2126 2.267 3.869 0.825\n+ 185HOH HW1 2127 2.349 3.869 0.882\n+ 185HOH HW2 2128 2.267 3.951 0.767\n+ 186HOH OW 2129 3.397 3.311 0.684\n+ 186HOH HW1 2130 3.478 3.311 0.741\n+ 186HOH HW2 2131 3.397 3.230 0.626\n+ 187HOH OW 2132 1.957 2.542 -0.142\n+ 187HOH HW1 2133 1.876 2.542 -0.084\n+ 187HOH HW2 2134 1.957 2.624 -0.200\n+ 188HOH OW 2135 1.479 1.567 0.726\n+ 188HOH HW1 2136 1.397 1.567 0.784\n+ 188HOH HW2 2137 1.479 1.486 0.668\n+ 189HOH OW 2138 1.911 2.802 -1.465\n+ 189HOH HW1 2139 1.911 2.884 -1.522\n+ 189HOH HW2 2140 1.911 2.721 -1.522\n+ 190HOH OW 2141 1.730 3.906 -1.245\n+ 190HOH HW1 2142 1.812 3.906 -1.188\n+ 190HOH HW2 2143 1.649 3.906 -1.188\n+ 191HOH OW 2144 1.620 1.450 0.558\n+ 191HOH HW1 2145 1.701 1.450 0.615\n+ 191HOH HW2 2146 1.620 1.532 0.500\n+ 192HOH OW 2147 1.735 4.635 -0.708\n+ 192HOH HW1 2148 1.816 4.635 -0.650\n+ 192HOH HW2 2149 1.735 4.553 -0.766\n+ 193HOH OW 2150 1.499 3.130 -0.424\n+ 193HOH HW1 2151 1.418 3.130 -0.366\n+ 193HOH HW2 2152 1.499 3.212 -0.482\n+ 194HOH OW 2153 2.820 4.477 -0.315\n+ 194HOH HW1 2154 2.738 4.477 -0.257\n+ 194HOH HW2 2155 2.820 4.396 -0.373\n+ 195HOH OW 2156 2.948 1.386 -0.911\n+ 195HOH HW1 2157 2.948 1.468 -0.968\n+ 195HOH HW2 2158 2.948 1.305 -0.968\n+ 196HOH OW 2159 2.361 4.481 0.261\n+ 196HOH HW1 2160 2.443 4.481 0.319\n+ 196HOH HW2 2161 2.280 4.481 0.319\n+ 197HOH OW 2162 4.057 2.218 -0.636\n+ 197HOH HW1 2163 4.139 2.218 -0.578\n+ 197HOH HW2 2164 4.057 2.300 -0.694\n+ 198HOH OW 2165 1.247 3.186 -0.623\n+ 198HOH HW1 2166 1.329 3.186 -0.565\n+ 198HOH HW2 2167 1.247 3.104 -0.680\n+ 199HOH OW 2168 1.668 1.359 -0.583\n+ 199HOH HW1 2169 1.587 1.359 -0.525\n+ 199HOH HW2 2170 1.668 1.441 -0.641\n+ 200HOH OW 2171 2.753 3.806 -1.286\n+ 200HOH HW1 2172 2.672 3.806 -1.228\n+ 200HOH HW2 2173 2.753 3.724 -1.344\n+ 201HOH OW 2174 2.589 3.597 1.156\n+ 201HOH HW1 2175 2.589 3.679 1.099\n+ 201HOH HW2 2176 2.589 3.516 1.099\n+ 202HOH OW 2177 2.479 2.518 1.606\n+ 202HOH HW1 2178 2.561 2.518 1.664\n+ 202HOH HW2 2179 2.397 2.518 1.664\n+ 203HOH OW 2180 1.258 2.121 0.501\n+ 203HOH HW1 2181 1.340 2.121 0.558\n+ 203HOH HW2 2182 1.258 2.203 0.443\n+ 204HOH OW 2183 1.969 2.375 -0.485\n+ 204HOH HW1 2184 2.050 2.375 -0.427\n+ 204HOH HW2 2185 1.969 2.293 -0.543\n+ 205HOH OW 2186 2.710 3.596 -1.236\n+ 205HOH HW1 2187 2.628 3.596 -1.178\n+ 205HOH HW2 2188 2.710 3.677 -1.294\n+ 206HOH OW 2189 3.726 0.963 1.000\n+ 206HOH HW1 2190 3.644 0.963 1.058\n+ 206HOH HW2 2191 3.726 0.882 0.942\n+ 207HOH OW 2192 4.376 2.384 0.804\n+ 207HOH HW1 2193 4.376 2.466 0.746\n+ 207HOH HW2 2194 4.376 2.303 0.746\n+ 5.90620 6.84510 3.05170\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/solv.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solv.gro Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,38395 @@\n+LYSOZYME\n+38392\n+ 1LYS N 1 4.434 3.396 2.469\n+ 1LYS H1 2 4.510 3.450 2.431\n+ 1LYS H2 3 4.368 3.376 2.397\n+ 1LYS H3 4 4.390 3.448 2.542\n+ 1LYS CA 5 4.487 3.269 2.524\n+ 1LYS HA 6 4.531 3.217 2.451\n+ 1LYS CB 7 4.585 3.306 2.636\n+ 1LYS HB1 8 4.661 3.357 2.597\n+ 1LYS HB2 9 4.537 3.363 2.703\n+ 1LYS CG 10 4.643 3.187 2.711\n+ 1LYS HG1 11 4.574 3.151 2.773\n+ 1LYS HG2 12 4.668 3.116 2.644\n+ 1LYS CD 13 4.767 3.227 2.790\n+ 1LYS HD1 14 4.843 3.245 2.727\n+ 1LYS HD2 15 4.747 3.309 2.843\n+ 1LYS CE 16 4.804 3.113 2.883\n+ 1LYS HE1 17 4.739 3.108 2.959\n+ 1LYS HE2 18 4.804 3.026 2.834\n+ 1LYS NZ 19 4.940 3.139 2.937\n+ 1LYS HZ1 20 4.967 3.065 2.999\n+ 1LYS HZ2 21 5.006 3.144 2.861\n+ 1LYS HZ3 22 4.940 3.226 2.987\n+ 1LYS C 23 4.372 3.188 2.583\n+ 1LYS O 24 4.293 3.243 2.659\n+ 2VAL N 25 4.372 3.058 2.563\n+ 2VAL H 26 4.434 3.022 2.493\n+ 2VAL CA 27 4.288 2.962 2.634\n+ 2VAL HA 28 4.215 3.014 2.677\n+ 2VAL CB 29 4.212 2.865 2.544\n+ 2VAL HB 30 4.284 2.814 2.497\n+ 2VAL CG1 31 4.123 2.770 2.624\n+ 2VAL HG11 32 4.075 2.709 2.561\n+ 2VAL HG12 33 4.180 2.717 2.686\n+ 2VAL HG13 34 4.056 2.823 2.676\n+ 2VAL CG2 35 4.127 2.933 2.438\n+ 2VAL HG21 36 4.081 2.864 2.383\n+ 2VAL HG22 37 4.060 2.992 2.482\n+ 2VAL HG23 38 4.186 2.989 2.379\n+ 2VAL C 39 4.378 2.893 2.738\n+ 2VAL O 40 4.474 2.823 2.701\n+ 3PHE N 41 4.347 2.917 2.863\n+ 3PHE H 42 4.273 2.981 2.883\n+ 3PHE CA 43 4.417 2.852 2.975\n+ 3PHE HA 44 4.513 2.859 2.950\n+ 3PHE CB 45 4.395 2.925 3.108\n+ 3PHE HB1 46 4.303 2.964 3.109\n+ 3PHE HB2 47 4.404 2.860 3.183\n+ 3PHE CG 48 4.492 3.036 3.129\n+ 3PHE CD1 49 4.465 3.167 3.087\n+ 3PHE HD1 50 4.379 3.187 3.040\n+ 3PHE CD2 51 4.598 3.018 3.220\n+ 3PHE HD2 52 4.611 2.928 3.262\n+ 3PHE CE1 53 4.556 3.270 3.110\n+ 3PHE HE1 54 4.546 3.357 3.063\n+ 3PHE CE2 55 4.685 3.121 3.251\n+ 3PHE HE2 56 4.764 3.104 3.310\n+ 3PHE CZ 57 4.662 3.249 3.200\n+ 3PHE HZ 58 4.720 3.326 3.228\n+ 3PHE C 59 4.372 2.706 2.990\n+ 3PHE O 60 4.250 2.678 2.981\n+ 4GLY N 61 4.470 2.626 3.034\n+ 4GLY H 62 4.565 2.657 3.035\n+ 4GLY CA 63 4.435 2.490 3.080\n+ 4GLY HA1 64 4.360 2.454 3.024\n+ 4GLY HA2 65 4.514 2.430 3.073\n+ 4GLY C 66 4.390 2.504 3.225\n+ 4GLY O 67 4.428 2.602 3.289\n+ 5ARG N 68 4.303 2.416 3.270\n+ 5ARG H 69 4.269 2.346 3.207\n+ 5ARG CA 70 4.254 2.416 3.408\n+ 5ARG HA 71 4.196 2.496 3.415\n+ 5ARG CB 72 4.174 2.288 3.434\n+ 5ARG HB1 73 4.098 2.284 3.370\n+ 5ARG HB2 74 4.234 2.209 3.420\n+ 5ARG CG 75 4.119 2.282 3.575\n+ 5ARG HG1 76 4.195 2.279 3.640\n+ 5ARG HG2 77 4.063 2.363 3.592\n+ 5ARG CD 78 4.036 2.162 3.595\n+ 5ARG HD1 79 4.002 2.161 3.689\n+ 5ARG HD2 80 3.958 2.167 3.532\n+ 5ARG NE 81 4.104 2.037 3.571\n+ 5ARG HE 82 4.100 2.002 3.478\n+ 5ARG CZ 83 4.171 1.963 3.657\n+ 5ARG NH1 84 4.182 1.995 3.786\n+ 5ARG HH11 85 4.137 2.078 3.820\n+ 5ARG HH12 86 4.234 1.937 3.848\n+ 5'..b'42 6.984\n+12245SOL HW138307 6.969 6.494 6.921\n+12245SOL HW238308 7.122 6.454 6.960\n+12246SOL OW38309 5.658 5.752 5.904\n+12246SOL HW138310 5.641 5.835 5.850\n+12246SOL HW238311 5.748 5.715 5.882\n+12247SOL OW38312 6.769 6.921 5.705\n+12247SOL HW138313 6.670 6.910 5.707\n+12247SOL HW238314 6.803 6.936 5.798\n+12248SOL OW38315 6.199 6.428 7.017\n+12248SOL HW138316 6.255 6.509 7.000\n+12248SOL HW238317 6.258 6.348 7.020\n+12249SOL OW38318 7.079 7.353 6.545\n+12249SOL HW138319 7.112 7.417 6.476\n+12249SOL HW238320 7.145 7.347 6.620\n+12250SOL OW38321 6.302 6.151 7.294\n+12250SOL HW138322 6.321 6.216 7.368\n+12250SOL HW238323 6.362 6.071 7.303\n+12251SOL OW38324 5.976 7.327 7.146\n+12251SOL HW138325 5.885 7.368 7.144\n+12251SOL HW238326 5.969 7.233 7.178\n+12252SOL OW38327 7.260 6.469 6.840\n+12252SOL HW138328 7.233 6.380 6.803\n+12252SOL HW238329 7.261 6.537 6.767\n+12253SOL OW38330 6.811 5.911 6.035\n+12253SOL HW138331 6.876 5.837 6.024\n+12253SOL HW238332 6.831 5.961 6.119\n+12254SOL OW38333 6.180 6.331 6.238\n+12254SOL HW138334 6.230 6.416 6.219\n+12254SOL HW238335 6.092 6.333 6.190\n+12255SOL OW38336 7.316 6.520 7.103\n+12255SOL HW138337 7.354 6.611 7.118\n+12255SOL HW238338 7.308 6.503 7.004\n+12256SOL OW38339 6.445 6.960 5.602\n+12256SOL HW138340 6.399 6.975 5.690\n+12256SOL HW238341 6.489 7.045 5.572\n+12257SOL OW38342 6.445 6.542 6.447\n+12257SOL HW138343 6.499 6.473 6.495\n+12257SOL HW238344 6.413 6.611 6.513\n+12258SOL OW38345 6.669 6.570 5.673\n+12258SOL HW138346 6.646 6.623 5.591\n+12258SOL HW238347 6.750 6.514 5.654\n+12259SOL OW38348 7.447 7.155 6.437\n+12259SOL HW138349 7.376 7.143 6.367\n+12259SOL HW238350 7.448 7.076 6.497\n+12260SOL OW38351 5.665 6.826 6.239\n+12260SOL HW138352 5.664 6.779 6.327\n+12260SOL HW238353 5.747 6.798 6.188\n+12261SOL OW38354 6.258 6.977 7.210\n+12261SOL HW138355 6.180 6.927 7.248\n+12261SOL HW238356 6.255 7.072 7.241\n+12262SOL OW38357 7.410 5.778 6.813\n+12262SOL HW138358 7.406 5.688 6.857\n+12262SOL HW238359 7.413 5.767 6.714\n+12263SOL OW38360 6.014 6.010 6.106\n+12263SOL HW138361 6.044 5.938 6.044\n+12263SOL HW238362 5.975 5.970 6.189\n+12264SOL OW38363 5.903 6.133 6.866\n+12264SOL HW138364 5.941 6.074 6.938\n+12264SOL HW238365 5.943 6.107 6.778\n+12265SOL OW38366 6.398 7.172 6.273\n+12265SOL HW138367 6.430 7.182 6.179\n+12265SOL HW238368 6.319 7.110 6.275\n+12266SOL OW38369 7.010 5.800 6.698\n+12266SOL HW138370 7.062 5.735 6.753\n+12266SOL HW238371 6.961 5.863 6.759\n+12267SOL OW38372 6.587 5.620 6.740\n+12267SOL HW138373 6.524 5.548 6.709\n+12267SOL HW238374 6.680 5.584 6.740\n+12268SOL OW38375 6.356 6.916 5.887\n+12268SOL HW138376 6.310 6.829 5.904\n+12268SOL HW238377 6.447 6.913 5.928\n+12269SOL OW38378 6.204 7.153 6.870\n+12269SOL HW138379 6.199 7.235 6.927\n+12269SOL HW238380 6.293 7.150 6.825\n+12270SOL OW38381 6.938 5.638 5.754\n+12270SOL HW138382 6.973 5.597 5.670\n+12270SOL HW238383 6.848 5.600 5.774\n+12271SOL OW38384 6.886 6.039 6.277\n+12271SOL HW138385 6.827 6.119 6.281\n+12271SOL HW238386 6.901 6.004 6.370\n+12272SOL OW38387 7.179 5.807 6.468\n+12272SOL HW138388 7.095 5.806 6.522\n+12272SOL HW238389 7.181 5.890 6.412\n+12273SOL OW38390 5.625 6.663 5.886\n+12273SOL HW138391 5.724 6.652 5.877\n+12273SOL HW238392 5.585 6.577 5.918\n+ 7.33925 7.33925 7.33925\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/solv_ions.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solv_ions.gro Thu Oct 04 17:38:27 2018 -0400 |
| b |
| b'@@ -0,0 +1,38379 @@\n+LYSOZYME in water\n+38376\n+ 1LYS N 1 4.434 3.396 2.469\n+ 1LYS H1 2 4.510 3.450 2.431\n+ 1LYS H2 3 4.368 3.376 2.397\n+ 1LYS H3 4 4.390 3.448 2.542\n+ 1LYS CA 5 4.487 3.269 2.524\n+ 1LYS HA 6 4.531 3.217 2.451\n+ 1LYS CB 7 4.585 3.306 2.636\n+ 1LYS HB1 8 4.661 3.357 2.597\n+ 1LYS HB2 9 4.537 3.363 2.703\n+ 1LYS CG 10 4.643 3.187 2.711\n+ 1LYS HG1 11 4.574 3.151 2.773\n+ 1LYS HG2 12 4.668 3.116 2.644\n+ 1LYS CD 13 4.767 3.227 2.790\n+ 1LYS HD1 14 4.843 3.245 2.727\n+ 1LYS HD2 15 4.747 3.309 2.843\n+ 1LYS CE 16 4.804 3.113 2.883\n+ 1LYS HE1 17 4.739 3.108 2.959\n+ 1LYS HE2 18 4.804 3.026 2.834\n+ 1LYS NZ 19 4.940 3.139 2.937\n+ 1LYS HZ1 20 4.967 3.065 2.999\n+ 1LYS HZ2 21 5.006 3.144 2.861\n+ 1LYS HZ3 22 4.940 3.226 2.987\n+ 1LYS C 23 4.372 3.188 2.583\n+ 1LYS O 24 4.293 3.243 2.659\n+ 2VAL N 25 4.372 3.058 2.563\n+ 2VAL H 26 4.434 3.022 2.493\n+ 2VAL CA 27 4.288 2.962 2.634\n+ 2VAL HA 28 4.215 3.014 2.677\n+ 2VAL CB 29 4.212 2.865 2.544\n+ 2VAL HB 30 4.284 2.814 2.497\n+ 2VAL CG1 31 4.123 2.770 2.624\n+ 2VAL HG11 32 4.075 2.709 2.561\n+ 2VAL HG12 33 4.180 2.717 2.686\n+ 2VAL HG13 34 4.056 2.823 2.676\n+ 2VAL CG2 35 4.127 2.933 2.438\n+ 2VAL HG21 36 4.081 2.864 2.383\n+ 2VAL HG22 37 4.060 2.992 2.482\n+ 2VAL HG23 38 4.186 2.989 2.379\n+ 2VAL C 39 4.378 2.893 2.738\n+ 2VAL O 40 4.474 2.823 2.701\n+ 3PHE N 41 4.347 2.917 2.863\n+ 3PHE H 42 4.273 2.981 2.883\n+ 3PHE CA 43 4.417 2.852 2.975\n+ 3PHE HA 44 4.513 2.859 2.950\n+ 3PHE CB 45 4.395 2.925 3.108\n+ 3PHE HB1 46 4.303 2.964 3.109\n+ 3PHE HB2 47 4.404 2.860 3.183\n+ 3PHE CG 48 4.492 3.036 3.129\n+ 3PHE CD1 49 4.465 3.167 3.087\n+ 3PHE HD1 50 4.379 3.187 3.040\n+ 3PHE CD2 51 4.598 3.018 3.220\n+ 3PHE HD2 52 4.611 2.928 3.262\n+ 3PHE CE1 53 4.556 3.270 3.110\n+ 3PHE HE1 54 4.546 3.357 3.063\n+ 3PHE CE2 55 4.685 3.121 3.251\n+ 3PHE HE2 56 4.764 3.104 3.310\n+ 3PHE CZ 57 4.662 3.249 3.200\n+ 3PHE HZ 58 4.720 3.326 3.228\n+ 3PHE C 59 4.372 2.706 2.990\n+ 3PHE O 60 4.250 2.678 2.981\n+ 4GLY N 61 4.470 2.626 3.034\n+ 4GLY H 62 4.565 2.657 3.035\n+ 4GLY CA 63 4.435 2.490 3.080\n+ 4GLY HA1 64 4.360 2.454 3.024\n+ 4GLY HA2 65 4.514 2.430 3.073\n+ 4GLY C 66 4.390 2.504 3.225\n+ 4GLY O 67 4.428 2.602 3.289\n+ 5ARG N 68 4.303 2.416 3.270\n+ 5ARG H 69 4.269 2.346 3.207\n+ 5ARG CA 70 4.254 2.416 3.408\n+ 5ARG HA 71 4.196 2.496 3.415\n+ 5ARG CB 72 4.174 2.288 3.434\n+ 5ARG HB1 73 4.098 2.284 3.370\n+ 5ARG HB2 74 4.234 2.209 3.420\n+ 5ARG CG 75 4.119 2.282 3.575\n+ 5ARG HG1 76 4.195 2.279 3.640\n+ 5ARG HG2 77 4.063 2.363 3.592\n+ 5ARG CD 78 4.036 2.162 3.595\n+ 5ARG HD1 79 4.002 2.161 3.689\n+ 5ARG HD2 80 3.958 2.167 3.532\n+ 5ARG NE 81 4.104 2.037 3.571\n+ 5ARG HE 82 4.100 2.002 3.478\n+ 5ARG CZ 83 4.171 1.963 3.657\n+ 5ARG NH1 84 4.182 1.995 3.786\n+ 5ARG HH11 85 4.137 2.078 3.820\n+ 5ARG HH12 86 4.234 1.937 3.8'..b'36 5.798\n+12240SOL OW38291 6.199 6.428 7.017\n+12240SOL HW138292 6.255 6.509 7.000\n+12240SOL HW238293 6.258 6.348 7.020\n+12241SOL OW38294 7.079 7.353 6.545\n+12241SOL HW138295 7.112 7.417 6.476\n+12241SOL HW238296 7.145 7.347 6.620\n+12242SOL OW38297 6.302 6.151 7.294\n+12242SOL HW138298 6.321 6.216 7.368\n+12242SOL HW238299 6.362 6.071 7.303\n+12243SOL OW38300 5.976 7.327 7.146\n+12243SOL HW138301 5.885 7.368 7.144\n+12243SOL HW238302 5.969 7.233 7.178\n+12244SOL OW38303 7.260 6.469 6.840\n+12244SOL HW138304 7.233 6.380 6.803\n+12244SOL HW238305 7.261 6.537 6.767\n+12245SOL OW38306 6.811 5.911 6.035\n+12245SOL HW138307 6.876 5.837 6.024\n+12245SOL HW238308 6.831 5.961 6.119\n+12246SOL OW38309 6.180 6.331 6.238\n+12246SOL HW138310 6.230 6.416 6.219\n+12246SOL HW238311 6.092 6.333 6.190\n+12247SOL OW38312 7.316 6.520 7.103\n+12247SOL HW138313 7.354 6.611 7.118\n+12247SOL HW238314 7.308 6.503 7.004\n+12248SOL OW38315 6.445 6.960 5.602\n+12248SOL HW138316 6.399 6.975 5.690\n+12248SOL HW238317 6.489 7.045 5.572\n+12249SOL OW38318 6.445 6.542 6.447\n+12249SOL HW138319 6.499 6.473 6.495\n+12249SOL HW238320 6.413 6.611 6.513\n+12250SOL OW38321 6.669 6.570 5.673\n+12250SOL HW138322 6.646 6.623 5.591\n+12250SOL HW238323 6.750 6.514 5.654\n+12251SOL OW38324 7.447 7.155 6.437\n+12251SOL HW138325 7.376 7.143 6.367\n+12251SOL HW238326 7.448 7.076 6.497\n+12252SOL OW38327 5.665 6.826 6.239\n+12252SOL HW138328 5.664 6.779 6.327\n+12252SOL HW238329 5.747 6.798 6.188\n+12253SOL OW38330 6.258 6.977 7.210\n+12253SOL HW138331 6.180 6.927 7.248\n+12253SOL HW238332 6.255 7.072 7.241\n+12254SOL OW38333 7.410 5.778 6.813\n+12254SOL HW138334 7.406 5.688 6.857\n+12254SOL HW238335 7.413 5.767 6.714\n+12255SOL OW38336 6.014 6.010 6.106\n+12255SOL HW138337 6.044 5.938 6.044\n+12255SOL HW238338 5.975 5.970 6.189\n+12256SOL OW38339 5.903 6.133 6.866\n+12256SOL HW138340 5.941 6.074 6.938\n+12256SOL HW238341 5.943 6.107 6.778\n+12257SOL OW38342 6.398 7.172 6.273\n+12257SOL HW138343 6.430 7.182 6.179\n+12257SOL HW238344 6.319 7.110 6.275\n+12258SOL OW38345 7.010 5.800 6.698\n+12258SOL HW138346 7.062 5.735 6.753\n+12258SOL HW238347 6.961 5.863 6.759\n+12259SOL OW38348 6.587 5.620 6.740\n+12259SOL HW138349 6.524 5.548 6.709\n+12259SOL HW238350 6.680 5.584 6.740\n+12260SOL OW38351 6.356 6.916 5.887\n+12260SOL HW138352 6.310 6.829 5.904\n+12260SOL HW238353 6.447 6.913 5.928\n+12261SOL OW38354 6.204 7.153 6.870\n+12261SOL HW138355 6.199 7.235 6.927\n+12261SOL HW238356 6.293 7.150 6.825\n+12262SOL OW38357 6.938 5.638 5.754\n+12262SOL HW138358 6.973 5.597 5.670\n+12262SOL HW238359 6.848 5.600 5.774\n+12263SOL OW38360 6.886 6.039 6.277\n+12263SOL HW138361 6.827 6.119 6.281\n+12263SOL HW238362 6.901 6.004 6.370\n+12264SOL OW38363 7.179 5.807 6.468\n+12264SOL HW138364 7.095 5.806 6.522\n+12264SOL HW238365 7.181 5.890 6.412\n+12265SOL OW38366 5.625 6.663 5.886\n+12265SOL HW138367 5.724 6.652 5.877\n+12265SOL HW238368 5.585 6.577 5.918\n+12266CL CL38369 0.197 2.838 1.264\n+12267CL CL38370 1.709 2.247 3.243\n+12268CL CL38371 1.576 7.248 4.031\n+12269CL CL38372 1.302 6.441 5.895\n+12270CL CL38373 3.133 3.659 6.177\n+12271CL CL38374 2.875 3.829 1.770\n+12272CL CL38375 7.275 0.922 0.612\n+12273CL CL38376 6.395 5.590 6.088\n+ 7.33925 7.33925 7.33925\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/topol.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol.top Thu Oct 04 17:38:27 2018 -0400 |
| [ |
| b'@@ -0,0 +1,18409 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-laptop\n+;\tAt date: Thu Aug 16 20:54:28 2018\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2018.2 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/gromacs2/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/gromacs2\n+;\tWorking dir: /home/simon/moldyn-galaxy/protein/test-data\n+;\tCommand line:\n+;\t gmx pdb2gmx -f 1AKI.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh\n+;\tForce field was read from the standard GROMACS share directory.\n+;\n+\n+; Include forcefield parameters\n+#include "oplsaa.ff/forcefield.itp"\n+\n+[ moleculetype ]\n+; Name nrexcl\n+Protein_chain_A 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n+; residue 1 LYS rtp LYSH q +2.0\n+ 1 opls_287 1 LYS N 1 -0.3 14.0027 ; qtot -0.3\n+ 2 opls_290 1 LYS H1 1 0.33 1.008 ; qtot 0.03\n+ 3 opls_290 1 LYS H2 1 0.33 1.008 ; qtot 0.36\n+ 4 opls_290 1 LYS H3 1 0.33 1.008 ; qtot 0.69\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011 ; qtot 0.94\n+ 6 opls_140 1 LYS HA 1 0.06 1.008 ; qtot 1\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011 ; qtot 0.88\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008 ; qtot 0.94\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008 ; qtot 1\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011 ; qtot 0.88\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008 ; qtot 0.94\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008 ; qtot 1\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011 ; qtot 0.88\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008 ; qtot 0.94\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008 ; qtot 1\n+ 16 opls_292 1 LYS CE 5 0.19 12.011 ; qtot 1.19\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008 ; qtot 1.25\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008 ; qtot 1.31\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067 ; qtot 1.01\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008 ; qtot 1.34\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008 ; qtot 1.67\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008 ; qtot 2\n+ 23 opls_235 1 LYS C 7 0.5 12.011 ; qtot 2.5\n+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n+; residue 2 VAL rtp VAL q 0.0\n+ 25 opls_238 2 VAL N 8 -0.5 14.0067 ; qtot 1.5\n+ 26 opls_241 2 VAL H 8 0.3 1.008 ; qtot 1.8\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011 ; qtot 1.94\n+ 28 opls_140 2 VAL HA 8 0.06 1.008 ; qtot 2\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011 ; qtot 1.94\n+ 30 opls_140 2 VAL HB 9 0.06 1.008 ; qtot 2\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011 ; qtot 1.82\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008 ; qtot 1.88\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008 ; qtot 1.94\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008 ; qtot 2\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011 ; qtot 1.82\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008 ; qtot 1.88\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008 ; qtot 1.9'..b'_Z_N_X_Y\n+ 1652 1659 1655 1656 1 improper_Z_CA_X_Y\n+ 1654 1653 1649 1657 1 improper_Z_CA_X_Y\n+ 1655 1657 1659 1660 1 improper_Z_CA_X_Y\n+ 1658 1657 1653 1659 1 improper_Z_CA_X_Y\n+ 1661 1665 1663 1664 1 improper_Z_N_X_Y\n+ 1665 1687 1685 1686 1 improper_O_C_X_Y\n+ 1673 1678 1676 1677 1 improper_Z_N_X_Y\n+ 1676 1679 1678 1682 1 improper_O_C_X_Y\n+ 1678 1680 1679 1681 1 improper_Z_N_X_Y\n+ 1678 1683 1682 1684 1 improper_Z_N_X_Y\n+ 1685 1689 1687 1688 1 improper_Z_N_X_Y\n+ 1689 1701 1699 1700 1 improper_O_C_X_Y\n+ 1691 1696 1694 1695 1 improper_O_C_X_Y\n+ 1694 1697 1696 1698 1 improper_Z_N_X_Y\n+ 1699 1703 1701 1702 1 improper_Z_N_X_Y\n+ 1703 1725 1723 1724 1 improper_O_C_X_Y\n+ 1711 1716 1714 1715 1 improper_Z_N_X_Y\n+ 1714 1717 1716 1720 1 improper_O_C_X_Y\n+ 1716 1718 1717 1719 1 improper_Z_N_X_Y\n+ 1716 1721 1720 1722 1 improper_Z_N_X_Y\n+ 1723 1727 1725 1726 1 improper_Z_N_X_Y\n+ 1727 1735 1733 1734 1 improper_O_C_X_Y\n+ 1733 1737 1735 1736 1 improper_Z_N_X_Y\n+ 1737 1757 1755 1756 1 improper_O_C_X_Y\n+ 1755 1759 1757 1758 1 improper_Z_N_X_Y\n+ 1759 1764 1762 1763 1 improper_O_C_X_Y\n+ 1762 1766 1764 1765 1 improper_Z_N_X_Y\n+ 1766 1778 1776 1777 1 improper_O_C_X_Y\n+ 1776 1780 1778 1779 1 improper_Z_N_X_Y\n+ 1780 1790 1788 1789 1 improper_O_C_X_Y\n+ 1782 1786 1785 1787 1 improper_O_C_X_Y\n+ 1788 1792 1790 1791 1 improper_Z_N_X_Y\n+ 1792 1806 1804 1805 1 improper_O_C_X_Y\n+ 1804 1808 1806 1807 1 improper_Z_N_X_Y\n+ 1808 1823 1821 1822 1 improper_O_C_X_Y\n+ 1813 1818 1816 1817 1 improper_O_C_X_Y\n+ 1816 1819 1818 1820 1 improper_Z_N_X_Y\n+ 1821 1825 1823 1824 1 improper_Z_N_X_Y\n+ 1825 1833 1831 1832 1 improper_O_C_X_Y\n+ 1831 1835 1833 1834 1 improper_Z_N_X_Y\n+ 1835 1857 1855 1856 1 improper_O_C_X_Y\n+ 1837 1840 1843 1841 1 improper_Z_CA_X_Y\n+ 1840 1844 1841 1842 1 improper_Z_CA_X_Y\n+ 1841 1846 1844 1845 1 improper_Z_N_X_Y\n+ 1846 1853 1849 1850 1 improper_Z_CA_X_Y\n+ 1848 1847 1843 1851 1 improper_Z_CA_X_Y\n+ 1849 1851 1853 1854 1 improper_Z_CA_X_Y\n+ 1852 1851 1847 1853 1 improper_Z_CA_X_Y\n+ 1855 1859 1857 1858 1 improper_Z_N_X_Y\n+ 1859 1876 1874 1875 1 improper_O_C_X_Y\n+ 1874 1878 1876 1877 1 improper_Z_N_X_Y\n+ 1878 1900 1898 1899 1 improper_O_C_X_Y\n+ 1886 1891 1889 1890 1 improper_Z_N_X_Y\n+ 1889 1892 1891 1895 1 improper_O_C_X_Y\n+ 1891 1893 1892 1894 1 improper_Z_N_X_Y\n+ 1891 1896 1895 1897 1 improper_Z_N_X_Y\n+ 1898 1902 1900 1901 1 improper_Z_N_X_Y\n+ 1902 1907 1905 1906 1 improper_O_C_X_Y\n+ 1905 1909 1907 1908 1 improper_Z_N_X_Y\n+ 1909 1917 1915 1916 1 improper_O_C_X_Y\n+ 1915 1919 1917 1918 1 improper_Z_N_X_Y\n+ 1919 1941 1939 1940 1 improper_O_C_X_Y\n+ 1927 1932 1930 1931 1 improper_Z_N_X_Y\n+ 1930 1933 1932 1936 1 improper_O_C_X_Y\n+ 1932 1934 1933 1935 1 improper_Z_N_X_Y\n+ 1932 1937 1936 1938 1 improper_Z_N_X_Y\n+ 1939 1943 1941 1942 1 improper_Z_N_X_Y\n+ 1943 1959 1958 1960 1 improper_O_C_X_Y\n+\n+; Include Position restraint file\n+#ifdef POSRES\n+#include "posres.itp"\n+#endif\n+\n+; Include water topology\n+#include "oplsaa.ff/spce.itp"\n+\n+#ifdef POSRES_WATER\n+; Position restraint for each water oxygen\n+[ position_restraints ]\n+; i funct fcx fcy fcz\n+ 1 1 1000 1000 1000\n+#endif\n+\n+; Include topology for ions\n+#include "oplsaa.ff/ions.itp"\n+\n+[ system ]\n+; Name\n+LYSOZYME\n+\n+[ molecules ]\n+; Compound #mols\n+Protein_chain_A 1\n+SOL 78\n' |
| b |
| diff -r 000000000000 -r 69ff679edefd test-data/topol_solv.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_solv.top Thu Oct 04 17:38:27 2018 -0400 |
| [ |
| b'@@ -0,0 +1,18411 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-laptop\n+;\tAt date: Thu Aug 16 20:54:28 2018\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2018.2 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/gromacs2/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/gromacs2\n+;\tWorking dir: /home/simon/moldyn-galaxy/protein/test-data\n+;\tCommand line:\n+;\t gmx pdb2gmx -f 1AKI.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh\n+;\tForce field was read from the standard GROMACS share directory.\n+;\n+\n+; Include forcefield parameters\n+#include "oplsaa.ff/forcefield.itp"\n+\n+[ moleculetype ]\n+; Name nrexcl\n+Protein_chain_A 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n+; residue 1 LYS rtp LYSH q +2.0\n+ 1 opls_287 1 LYS N 1 -0.3 14.0027 ; qtot -0.3\n+ 2 opls_290 1 LYS H1 1 0.33 1.008 ; qtot 0.03\n+ 3 opls_290 1 LYS H2 1 0.33 1.008 ; qtot 0.36\n+ 4 opls_290 1 LYS H3 1 0.33 1.008 ; qtot 0.69\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011 ; qtot 0.94\n+ 6 opls_140 1 LYS HA 1 0.06 1.008 ; qtot 1\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011 ; qtot 0.88\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008 ; qtot 0.94\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008 ; qtot 1\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011 ; qtot 0.88\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008 ; qtot 0.94\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008 ; qtot 1\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011 ; qtot 0.88\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008 ; qtot 0.94\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008 ; qtot 1\n+ 16 opls_292 1 LYS CE 5 0.19 12.011 ; qtot 1.19\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008 ; qtot 1.25\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008 ; qtot 1.31\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067 ; qtot 1.01\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008 ; qtot 1.34\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008 ; qtot 1.67\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008 ; qtot 2\n+ 23 opls_235 1 LYS C 7 0.5 12.011 ; qtot 2.5\n+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n+; residue 2 VAL rtp VAL q 0.0\n+ 25 opls_238 2 VAL N 8 -0.5 14.0067 ; qtot 1.5\n+ 26 opls_241 2 VAL H 8 0.3 1.008 ; qtot 1.8\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011 ; qtot 1.94\n+ 28 opls_140 2 VAL HA 8 0.06 1.008 ; qtot 2\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011 ; qtot 1.94\n+ 30 opls_140 2 VAL HB 9 0.06 1.008 ; qtot 2\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011 ; qtot 1.82\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008 ; qtot 1.88\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008 ; qtot 1.94\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008 ; qtot 2\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011 ; qtot 1.82\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008 ; qtot 1.88\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008 ; qtot 1.9'..b'per_Z_CA_X_Y\n+ 1654 1653 1649 1657 1 improper_Z_CA_X_Y\n+ 1655 1657 1659 1660 1 improper_Z_CA_X_Y\n+ 1658 1657 1653 1659 1 improper_Z_CA_X_Y\n+ 1661 1665 1663 1664 1 improper_Z_N_X_Y\n+ 1665 1687 1685 1686 1 improper_O_C_X_Y\n+ 1673 1678 1676 1677 1 improper_Z_N_X_Y\n+ 1676 1679 1678 1682 1 improper_O_C_X_Y\n+ 1678 1680 1679 1681 1 improper_Z_N_X_Y\n+ 1678 1683 1682 1684 1 improper_Z_N_X_Y\n+ 1685 1689 1687 1688 1 improper_Z_N_X_Y\n+ 1689 1701 1699 1700 1 improper_O_C_X_Y\n+ 1691 1696 1694 1695 1 improper_O_C_X_Y\n+ 1694 1697 1696 1698 1 improper_Z_N_X_Y\n+ 1699 1703 1701 1702 1 improper_Z_N_X_Y\n+ 1703 1725 1723 1724 1 improper_O_C_X_Y\n+ 1711 1716 1714 1715 1 improper_Z_N_X_Y\n+ 1714 1717 1716 1720 1 improper_O_C_X_Y\n+ 1716 1718 1717 1719 1 improper_Z_N_X_Y\n+ 1716 1721 1720 1722 1 improper_Z_N_X_Y\n+ 1723 1727 1725 1726 1 improper_Z_N_X_Y\n+ 1727 1735 1733 1734 1 improper_O_C_X_Y\n+ 1733 1737 1735 1736 1 improper_Z_N_X_Y\n+ 1737 1757 1755 1756 1 improper_O_C_X_Y\n+ 1755 1759 1757 1758 1 improper_Z_N_X_Y\n+ 1759 1764 1762 1763 1 improper_O_C_X_Y\n+ 1762 1766 1764 1765 1 improper_Z_N_X_Y\n+ 1766 1778 1776 1777 1 improper_O_C_X_Y\n+ 1776 1780 1778 1779 1 improper_Z_N_X_Y\n+ 1780 1790 1788 1789 1 improper_O_C_X_Y\n+ 1782 1786 1785 1787 1 improper_O_C_X_Y\n+ 1788 1792 1790 1791 1 improper_Z_N_X_Y\n+ 1792 1806 1804 1805 1 improper_O_C_X_Y\n+ 1804 1808 1806 1807 1 improper_Z_N_X_Y\n+ 1808 1823 1821 1822 1 improper_O_C_X_Y\n+ 1813 1818 1816 1817 1 improper_O_C_X_Y\n+ 1816 1819 1818 1820 1 improper_Z_N_X_Y\n+ 1821 1825 1823 1824 1 improper_Z_N_X_Y\n+ 1825 1833 1831 1832 1 improper_O_C_X_Y\n+ 1831 1835 1833 1834 1 improper_Z_N_X_Y\n+ 1835 1857 1855 1856 1 improper_O_C_X_Y\n+ 1837 1840 1843 1841 1 improper_Z_CA_X_Y\n+ 1840 1844 1841 1842 1 improper_Z_CA_X_Y\n+ 1841 1846 1844 1845 1 improper_Z_N_X_Y\n+ 1846 1853 1849 1850 1 improper_Z_CA_X_Y\n+ 1848 1847 1843 1851 1 improper_Z_CA_X_Y\n+ 1849 1851 1853 1854 1 improper_Z_CA_X_Y\n+ 1852 1851 1847 1853 1 improper_Z_CA_X_Y\n+ 1855 1859 1857 1858 1 improper_Z_N_X_Y\n+ 1859 1876 1874 1875 1 improper_O_C_X_Y\n+ 1874 1878 1876 1877 1 improper_Z_N_X_Y\n+ 1878 1900 1898 1899 1 improper_O_C_X_Y\n+ 1886 1891 1889 1890 1 improper_Z_N_X_Y\n+ 1889 1892 1891 1895 1 improper_O_C_X_Y\n+ 1891 1893 1892 1894 1 improper_Z_N_X_Y\n+ 1891 1896 1895 1897 1 improper_Z_N_X_Y\n+ 1898 1902 1900 1901 1 improper_Z_N_X_Y\n+ 1902 1907 1905 1906 1 improper_O_C_X_Y\n+ 1905 1909 1907 1908 1 improper_Z_N_X_Y\n+ 1909 1917 1915 1916 1 improper_O_C_X_Y\n+ 1915 1919 1917 1918 1 improper_Z_N_X_Y\n+ 1919 1941 1939 1940 1 improper_O_C_X_Y\n+ 1927 1932 1930 1931 1 improper_Z_N_X_Y\n+ 1930 1933 1932 1936 1 improper_O_C_X_Y\n+ 1932 1934 1933 1935 1 improper_Z_N_X_Y\n+ 1932 1937 1936 1938 1 improper_Z_N_X_Y\n+ 1939 1943 1941 1942 1 improper_Z_N_X_Y\n+ 1943 1959 1958 1960 1 improper_O_C_X_Y\n+\n+; Include Position restraint file\n+#ifdef POSRES\n+#include "posres.itp"\n+#endif\n+\n+; Include water topology\n+#include "oplsaa.ff/spce.itp"\n+\n+#ifdef POSRES_WATER\n+; Position restraint for each water oxygen\n+[ position_restraints ]\n+; i funct fcx fcy fcz\n+ 1 1 1000 1000 1000\n+#endif\n+\n+; Include topology for ions\n+#include "oplsaa.ff/ions.itp"\n+\n+[ system ]\n+; Name\n+LYSOZYME in water\n+\n+[ molecules ]\n+; Compound #mols\n+Protein_chain_A 1\n+SOL 78\n+SOL 12058\n+CL 8\n' |