| Next changeset 1:e9cc595562b8 (2020-02-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1" |
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added:
macros.xml merge_top.py test-data/1AKI.pdb test-data/em.edr test-data/em.gro test-data/em.tpr test-data/em.trr test-data/index.ndx 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.ndx 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/md_0_1.xvg 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/posre_cl.itp test-data/posres.itp test-data/processed.gro test-data/solv.gro test-data/solv_ions.gro test-data/top_output.top test-data/topol.top test-data/topol_solv.top test-data/trjcat.xtc test-data/trjconv.xtc trj.xml |
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| diff -r 000000000000 -r bb0053c4e4f2 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jan 21 07:29:43 2020 -0500 |
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| @@ -0,0 +1,84 @@ +<macros> + <token name="@VERSION@">2019.1.4</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2019.1">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 simulation" value="0" min="0" max="1000000" help="NPT steps" /> + + </when> + + </conditional> + + </xml> + + <xml name="log"> + <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="log_outputs"> + <data name="report" format="txt" from_work_dir="verbose.txt"> + <filter>capture_log</filter> + </data> + </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 bb0053c4e4f2 merge_top.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merge_top.py Tue Jan 21 07:29:43 2020 -0500 |
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| @@ -0,0 +1,38 @@ +import re +import sys + + +def combine_tops(top_text, itp_texts): + """ + Search through parent topology top_text and replace + #include lines with the relevant child topologies + from the dictionary itp_texts + """ + for itp in itp_texts: + # split on include string, then rejoin around itp file + spl = re.split('#include ".*{}"\n'.format(itp), top_text) + top_text = itp_texts[itp].join(spl) + return top_text + + +top = sys.argv[1] # parent topology file +itps_file = sys.argv[2] # file with list of child topologies (.itp files) + +with open(itps_file) as f: + itps = f.read().split() + +with open(top, 'r') as f: + top_text = f.read() + +itp_texts = {} # create dictionary of child topologies +for itp in itps: + with open(itp, 'r') as f: + itp_texts[itp] = f.read() + +for itp in itp_texts: + # child tops may also refer to each other; we need to check this + itp_texts[itp] = combine_tops(itp_texts[itp], itp_texts) + +with open('top_output.top', 'w') as f: + # now combine all children into the parent + f.write(combine_tops(top_text, itp_texts)) |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/1AKI.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1AKI.pdb Tue Jan 21 07:29:43 2020 -0500 |
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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 bb0053c4e4f2 test-data/em.edr |
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| Binary file test-data/em.edr has changed |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/em.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/em.gro Tue Jan 21 07:29:43 2020 -0500 |
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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' |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/em.tpr |
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| Binary file test-data/em.tpr has changed |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/em.trr |
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| Binary file test-data/em.trr has changed |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/index.ndx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/index.ndx Tue Jan 21 07:29:43 2020 -0500 |
| [ |
| b'@@ -0,0 +1,13162 @@\n+[ System ]\n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15\n+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30\n+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45\n+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60\n+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75\n+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\n+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105\n+ 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120\n+ 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135\n+ 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150\n+ 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165\n+ 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180\n+ 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195\n+ 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210\n+ 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225\n+ 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240\n+ 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255\n+ 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270\n+ 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285\n+ 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300\n+ 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315\n+ 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330\n+ 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345\n+ 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360\n+ 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375\n+ 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390\n+ 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405\n+ 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420\n+ 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435\n+ 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450\n+ 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465\n+ 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480\n+ 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495\n+ 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510\n+ 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525\n+ 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540\n+ 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555\n+ 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570\n+ 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585\n+ 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600\n+ 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615\n+ 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630\n+ 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645\n+ 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660\n+ 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675\n+ 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690\n+ 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705\n+ 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720\n+ 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735\n+ 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750\n+ 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765\n+ 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780\n+ 781 782 783'..b'1 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185\n+1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200\n+1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215\n+1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230\n+1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245\n+1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260\n+1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275\n+1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290\n+1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305\n+1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320\n+1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335\n+1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350\n+1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365\n+1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380\n+1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395\n+1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410\n+1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425\n+1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440\n+1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455\n+1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470\n+1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485\n+1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500\n+1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515\n+1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530\n+1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545\n+1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560\n+1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575\n+1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590\n+1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605\n+1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620\n+1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635\n+1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650\n+1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665\n+1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680\n+1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695\n+1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710\n+1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725\n+1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740\n+1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755\n+1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770\n+1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785\n+1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800\n+1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815\n+1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830\n+1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845\n+1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860\n+1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875\n+1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890\n+1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905\n+1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920\n+1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935\n+1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950\n+1951 1952 1953 1954 1955 1956 1957 1958 1959 1960\n' |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/ions.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ions.mdp Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/ions.tpr |
| b |
| Binary file test-data/ions.tpr has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/md.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md.mdp Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/md_0_1.cpt |
| b |
| Binary file test-data/md_0_1.cpt has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/md_0_1.edr |
| b |
| Binary file test-data/md_0_1.edr has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/md_0_1.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md_0_1.gro Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/md_0_1.ndx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md_0_1.ndx Tue Jan 21 07:29:43 2020 -0500 |
| [ |
| b'@@ -0,0 +1,13032 @@\n+[ System ]\n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15\n+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30\n+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45\n+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60\n+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75\n+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\n+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105\n+ 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120\n+ 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135\n+ 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150\n+ 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165\n+ 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180\n+ 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195\n+ 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210\n+ 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225\n+ 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240\n+ 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255\n+ 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270\n+ 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285\n+ 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300\n+ 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315\n+ 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330\n+ 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345\n+ 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360\n+ 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375\n+ 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390\n+ 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405\n+ 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420\n+ 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435\n+ 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450\n+ 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465\n+ 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480\n+ 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495\n+ 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510\n+ 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525\n+ 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540\n+ 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555\n+ 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570\n+ 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585\n+ 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600\n+ 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615\n+ 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630\n+ 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645\n+ 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660\n+ 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675\n+ 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690\n+ 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705\n+ 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720\n+ 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735\n+ 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750\n+ 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765\n+ 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780\n+ 781 782 783'..b'7730 37731 37732 37733 37734 37735\n+37736 37737 37738 37739 37740 37741 37742 37743 37744 37745 37746 37747 37748 37749 37750\n+37751 37752 37753 37754 37755 37756 37757 37758 37759 37760 37761 37762 37763 37764 37765\n+37766 37767 37768 37769 37770 37771 37772 37773 37774 37775 37776 37777 37778 37779 37780\n+37781 37782 37783 37784 37785 37786 37787 37788 37789 37790 37791 37792 37793 37794 37795\n+37796 37797 37798 37799 37800 37801 37802 37803 37804 37805 37806 37807 37808 37809 37810\n+37811 37812 37813 37814 37815 37816 37817 37818 37819 37820 37821 37822 37823 37824 37825\n+37826 37827 37828 37829 37830 37831 37832 37833 37834 37835 37836 37837 37838 37839 37840\n+37841 37842 37843 37844 37845 37846 37847 37848 37849 37850 37851 37852 37853 37854 37855\n+37856 37857 37858 37859 37860 37861 37862 37863 37864 37865 37866 37867 37868 37869 37870\n+37871 37872 37873 37874 37875 37876 37877 37878 37879 37880 37881 37882 37883 37884 37885\n+37886 37887 37888 37889 37890 37891 37892 37893 37894 37895 37896 37897 37898 37899 37900\n+37901 37902 37903 37904 37905 37906 37907 37908 37909 37910 37911 37912 37913 37914 37915\n+37916 37917 37918 37919 37920 37921 37922 37923 37924 37925 37926 37927 37928 37929 37930\n+37931 37932 37933 37934 37935 37936 37937 37938 37939 37940 37941 37942 37943 37944 37945\n+37946 37947 37948 37949 37950 37951 37952 37953 37954 37955 37956 37957 37958 37959 37960\n+37961 37962 37963 37964 37965 37966 37967 37968 37969 37970 37971 37972 37973 37974 37975\n+37976 37977 37978 37979 37980 37981 37982 37983 37984 37985 37986 37987 37988 37989 37990\n+37991 37992 37993 37994 37995 37996 37997 37998 37999 38000 38001 38002 38003 38004 38005\n+38006 38007 38008 38009 38010 38011 38012 38013 38014 38015 38016 38017 38018 38019 38020\n+38021 38022 38023 38024 38025 38026 38027 38028 38029 38030 38031 38032 38033 38034 38035\n+38036 38037 38038 38039 38040 38041 38042 38043 38044 38045 38046 38047 38048 38049 38050\n+38051 38052 38053 38054 38055 38056 38057 38058 38059 38060 38061 38062 38063 38064 38065\n+38066 38067 38068 38069 38070 38071 38072 38073 38074 38075 38076 38077 38078 38079 38080\n+38081 38082 38083 38084 38085 38086 38087 38088 38089 38090 38091 38092 38093 38094 38095\n+38096 38097 38098 38099 38100 38101 38102 38103 38104 38105 38106 38107 38108 38109 38110\n+38111 38112 38113 38114 38115 38116 38117 38118 38119 38120 38121 38122 38123 38124 38125\n+38126 38127 38128 38129 38130 38131 38132 38133 38134 38135 38136 38137 38138 38139 38140\n+38141 38142 38143 38144 38145 38146 38147 38148 38149 38150 38151 38152 38153 38154 38155\n+38156 38157 38158 38159 38160 38161 38162 38163 38164 38165 38166 38167 38168 38169 38170\n+38171 38172 38173 38174 38175 38176 38177 38178 38179 38180 38181 38182 38183 38184 38185\n+38186 38187 38188 38189 38190 38191 38192 38193 38194 38195 38196 38197 38198 38199 38200\n+38201 38202 38203 38204 38205 38206 38207 38208 38209 38210 38211 38212 38213 38214 38215\n+38216 38217 38218 38219 38220 38221 38222 38223 38224 38225 38226 38227 38228 38229 38230\n+38231 38232 38233 38234 38235 38236 38237 38238 38239 38240 38241 38242 38243 38244 38245\n+38246 38247 38248 38249 38250 38251 38252 38253 38254 38255 38256 38257 38258 38259 38260\n+38261 38262 38263 38264 38265 38266 38267 38268 38269 38270 38271 38272 38273 38274 38275\n+38276 38277 38278 38279 38280 38281 38282 38283 38284 38285 38286 38287 38288 38289 38290\n+38291 38292 38293 38294 38295 38296 38297 38298 38299 38300 38301 38302 38303 38304 38305\n+38306 38307 38308 38309 38310 38311 38312 38313 38314 38315 38316 38317 38318 38319 38320\n+38321 38322 38323 38324 38325 38326 38327 38328 38329 38330 38331 38332 38333 38334 38335\n+38336 38337 38338 38339 38340 38341 38342 38343 38344 38345 38346 38347 38348 38349 38350\n+38351 38352 38353 38354 38355 38356 38357 38358 38359 38360 38361 38362 38363 38364 38365\n+38366 38367 38368 38369 38370 38371 38372 38373 38374 38375 38376\n+[ !Protein_&_non-Water ]\n+38369 38370 38371 38372 38373 38374 38375 38376\n' |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/md_0_1.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md_0_1.pdb Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/md_0_1.tpr |
| b |
| Binary file test-data/md_0_1.tpr has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/md_0_1.trr |
| b |
| Binary file test-data/md_0_1.trr has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/md_0_1.xtc |
| b |
| Binary file test-data/md_0_1.xtc has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/md_0_1.xvg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md_0_1.xvg Tue Jan 21 07:29:43 2020 -0500 |
| b |
| @@ -0,0 +1,37 @@ +# This file was created Sat Nov 9 15:20:20 2019 +# Created by: +# :-) GROMACS - gmx energy, 2019.1 (-: +# +# Executable: /home/simon/miniconda3/envs/gmx/bin/gmx +# Data prefix: /home/simon/miniconda3/envs/gmx +# Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/gromacs +# Command line: +# gmx energy -f test-data/md_0_1.edr -o xvg5.xvg +# gmx energy is part of G R O M A C S: +# +# Gromacs Runs One Microsecond At Cannonball Speeds +# +@ title "GROMACS Energies" +@ xaxis label "Time (ps)" +@ yaxis label "(kJ/mol), (K)" +@TYPE xy +@ view 0.15, 0.15, 0.75, 0.85 +@ legend on +@ legend box on +@ legend loctype view +@ legend 0.78, 0.8 +@ legend length 2 +@ s0 legend "Potential" +@ s1 legend "Total Energy" +@ s2 legend "Temperature" + 0.000000 -593300.312500 -497358.281250 300.761719 + 0.100000 -592522.125000 -497450.843750 298.032074 + 0.200000 -593496.500000 -497942.718750 299.544647 + 0.300000 -593921.062500 -497878.187500 301.077850 + 0.400000 -593262.062500 -497926.406250 298.860870 + 0.500000 -593674.437500 -498809.312500 297.385773 + 0.600000 -594222.062500 -498825.562500 299.051605 + 0.700000 -593496.625000 -498020.125000 299.302399 + 0.800000 -593813.875000 -498131.031250 299.949219 + 0.900000 -594351.437500 -498515.812500 300.428131 + 1.000000 -595232.000000 -499672.000000 299.564087 |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/minim.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minim.mdp Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/newbox.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/newbox.gro Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/npt.cpt |
| b |
| Binary file test-data/npt.cpt has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/npt.edr |
| b |
| Binary file test-data/npt.edr has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/npt.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/npt.gro Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/npt.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/npt.mdp Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/npt.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/npt.pdb Tue Jan 21 07:29:43 2020 -0500 |
| 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' |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/npt.tpr |
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| Binary file test-data/npt.tpr has changed |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/npt.trr |
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| Binary file test-data/npt.trr has changed |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/npt.xtc |
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| Binary file test-data/npt.xtc has changed |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/nvt.cpt |
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| Binary file test-data/nvt.cpt has changed |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/nvt.edr |
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| Binary file test-data/nvt.edr has changed |
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| diff -r 000000000000 -r bb0053c4e4f2 test-data/nvt.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nvt.gro Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/nvt.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nvt.mdp Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/nvt.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nvt.pdb Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/nvt.tpr |
| b |
| Binary file test-data/nvt.tpr has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/nvt.trr |
| b |
| Binary file test-data/nvt.trr has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/nvt.xtc |
| b |
| Binary file test-data/nvt.xtc has changed |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/posre_cl.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posre_cl.itp Tue Jan 21 07:29:43 2020 -0500 |
| [ |
| @@ -0,0 +1,12 @@ +; position restraints for CL of LYSOZYME in water + +[ position_restraints ] +; i funct fcx fcy fcz +38369 1 500 600 700 +38370 1 500 600 700 +38371 1 500 600 700 +38372 1 500 600 700 +38373 1 500 600 700 +38374 1 500 600 700 +38375 1 500 600 700 +38376 1 500 600 700 |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/posres.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posres.itp Tue Jan 21 07:29:43 2020 -0500 |
| [ |
| 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 bb0053c4e4f2 test-data/processed.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/processed.gro Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/solv.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solv.gro Tue Jan 21 07:29:43 2020 -0500 |
| 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 bb0053c4e4f2 test-data/solv_ions.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solv_ions.gro Tue Jan 21 07:29:43 2020 -0500 |
| 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 1.638 2.961 6.665\n+12267CL CL38370 1.014 5.822 2.833\n+12268CL CL38371 4.539 0.572 5.911\n+12269CL CL38372 4.031 3.787 0.618\n+12270CL CL38373 4.492 4.868 4.747\n+12271CL CL38374 5.835 5.509 4.965\n+12272CL CL38375 6.974 7.159 0.477\n+12273CL CL38376 7.044 6.321 2.590\n+ 7.33925 7.33925 7.33925\n' |
| b |
| diff -r 000000000000 -r bb0053c4e4f2 test-data/top_output.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/top_output.top Tue Jan 21 07:29:43 2020 -0500 |
| [ |
| b'@@ -0,0 +1,19416 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-notebook\n+;\tAt date: Wed Aug 28 14:35:18 2019\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/gmx/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/gmx\n+;\tWorking dir: /home/simon/Repos/galaxy-tools-compchem/tools/gromacs\n+;\tCommand line:\n+;\t gmx pdb2gmx -f test-data/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\n+ 2 opls_290 1 LYS H1 1 0.33 1.008\n+ 3 opls_290 1 LYS H2 1 0.33 1.008\n+ 4 opls_290 1 LYS H3 1 0.33 1.008\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011\n+ 6 opls_140 1 LYS HA 1 0.06 1.008\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008\n+ 16 opls_292 1 LYS CE 5 0.19 12.011\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008\n+ 23 opls_235 1 LYS C 7 0.5 12.011\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\n+ 26 opls_241 2 VAL H 8 0.3 1.008\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011\n+ 28 opls_140 2 VAL HA 8 0.06 1.008\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011\n+ 30 opls_140 2 VAL HB 9 0.06 1.008\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008\n+ 38 opls_140 2 VAL HG23 11 0.06 1.008\n+ 39 opls_235 2 VAL C 12 0.5 12.011\n+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2\n+; residue 3 PHE rtp PHE q 0.0\n+ 41 opls_238 3 PHE N 13 -0.5 14.0067\n+ 42 opls_241 3 PHE H 13 0.3 1.008\n+ 43 opls_224B 3 PHE CA 13 0.14 12.011\n+ '..b'000 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+#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 bb0053c4e4f2 test-data/topol.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol.top Tue Jan 21 07:29:43 2020 -0500 |
| [ |
| b'@@ -0,0 +1,18409 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-notebook\n+;\tAt date: Wed Aug 28 14:35:18 2019\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/gmx/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/gmx\n+;\tWorking dir: /home/simon/Repos/galaxy-tools-compchem/tools/gromacs\n+;\tCommand line:\n+;\t gmx pdb2gmx -f test-data/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\n+ 2 opls_290 1 LYS H1 1 0.33 1.008\n+ 3 opls_290 1 LYS H2 1 0.33 1.008\n+ 4 opls_290 1 LYS H3 1 0.33 1.008\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011\n+ 6 opls_140 1 LYS HA 1 0.06 1.008\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008\n+ 16 opls_292 1 LYS CE 5 0.19 12.011\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008\n+ 23 opls_235 1 LYS C 7 0.5 12.011\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\n+ 26 opls_241 2 VAL H 8 0.3 1.008\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011\n+ 28 opls_140 2 VAL HA 8 0.06 1.008\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011\n+ 30 opls_140 2 VAL HB 9 0.06 1.008\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008\n+ 38 opls_140 2 VAL HG23 11 0.06 1.008\n+ 39 opls_235 2 VAL C 12 0.5 12.011\n+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2\n+; residue 3 PHE rtp PHE q 0.0\n+ 41 opls_238 3 PHE N 13 -0.5 14.0067\n+ 42 opls_241 3 PHE H 13 0.3 1.008\n+ 43 opls_224B 3 PHE CA 13 0.14 12.011\n+ '..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 bb0053c4e4f2 test-data/topol_solv.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_solv.top Tue Jan 21 07:29:43 2020 -0500 |
| [ |
| b'@@ -0,0 +1,18411 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-notebook\n+;\tAt date: Wed Aug 28 14:35:18 2019\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/gmx/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/gmx\n+;\tWorking dir: /home/simon/Repos/galaxy-tools-compchem/tools/gromacs\n+;\tCommand line:\n+;\t gmx pdb2gmx -f test-data/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\n+ 2 opls_290 1 LYS H1 1 0.33 1.008\n+ 3 opls_290 1 LYS H2 1 0.33 1.008\n+ 4 opls_290 1 LYS H3 1 0.33 1.008\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011\n+ 6 opls_140 1 LYS HA 1 0.06 1.008\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008\n+ 16 opls_292 1 LYS CE 5 0.19 12.011\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008\n+ 23 opls_235 1 LYS C 7 0.5 12.011\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\n+ 26 opls_241 2 VAL H 8 0.3 1.008\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011\n+ 28 opls_140 2 VAL HA 8 0.06 1.008\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011\n+ 30 opls_140 2 VAL HB 9 0.06 1.008\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008\n+ 38 opls_140 2 VAL HG23 11 0.06 1.008\n+ 39 opls_235 2 VAL C 12 0.5 12.011\n+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2\n+; residue 3 PHE rtp PHE q 0.0\n+ 41 opls_238 3 PHE N 13 -0.5 14.0067\n+ 42 opls_241 3 PHE H 13 0.3 1.008\n+ 43 opls_224B 3 PHE CA 13 0.14 12.011\n+ '..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' |
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| b'@@ -0,0 +1,177 @@\n+<tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@VERSION@">\n+ <description>using trjconv and trjcat</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements" />\n+\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+ #if $trj.trj_op == \'trjcat\':\n+ mkdir trajs &&\n+ #for $value, $file in enumerate($trj_input):\n+ ln -s \'$file\' trajs/traj_${value}.${file.ext} &&\n+ #end for\n+\n+ gmx trjcat\n+ -f trajs/traj* ## here we assume that they all have the same ext, probably reasonable\n+ $trj.cat\n+ -e \'$time.e\'\n+\n+ #elif $trj.trj_op == \'trjconv\':\n+ ln -s \'$ndx_input\' ./index.ndx &&\n+ ln -s \'$str_input\' ./str.${str_input.ext} &&\n+ ln -s \'$trj_input\' ./traj.${trj_input.ext} &&\n+ #if $trj.center:\n+ echo \'$trj.index_center $trj.index_output\' | gmx trjconv\n+ #else\n+ echo \'$trj.index_output\' | gmx trjconv\n+ #end if\n+ -f ./traj.${trj_input.ext}\n+ -s ./str.${str_input.ext}\n+ -n ./index.ndx\n+ $trj.center\n+ -pbc $trj.pbc\n+ -ur $trj.ur\n+ -boxcenter $trj.boxcenter\n+ #if $time.e != -1:\n+ -e \'$time.e\'\n+ #end if\n+\n+ #end if\n+\n+ -b \'$time.b\'\n+ -dt \'$time.dt\'\n+ -o ./output.${output_format} &&\n+ \n+ mv ./output.${output_format} \'$output\'\n+\n+ ]]></command>\n+\n+ <inputs>\n+ <conditional name="trj">\n+ <param name="trj_op" type="select" label="Modify a trajectory or concatenate multiple trajectories?">\n+ <option value="trjconv">Modify (trjconv)</option>\n+ <option value="trjcat">Concatenate (trjcat)</option>\n+ </param>\n+ <when value="trjconv">\n+ <param name="trj_input" type="data" format=\'xtc,trr\' label="Input trajectory" help="In XTC or TRR format."/>\n+ <param name="str_input" type="data" format=\'pdb,gro,tpr\' label="Input structure" help="In PDB, GRO or TPR format."/>\n+ <param name="ndx_input" type="data" format=\'ndx\' label="Index (NDX) file" help="In NDX format."/>\n+ <param name="index_output" type="text" label="Index of group to save in the output" help="Index of group to save in the output - i.e. the group\'s position in the ndx file (using zero-based numbering, so the first group has index 0).">\n+ <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>\n+ </param>\n+ <param name="center" type="boolean" label="Center system in box" truevalue="-center" falsevalue=""/>\n+ <param name="index_center" type="text" label="Index of group for centering" optional="true" help="Index of group for centering - i.e. the group\'s position in the ndx file (using zero-based numbering, so the first group has index 0). Leave blank if centering is not required.">\n+ <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>\n+ </param>\n+ <param name="pbc" type="select" label="PBC treatment" >\n+ <option value="none">none</option>\n+ <option value="mol">mol</option>\n+ <option value="res">res</option>\n+ <option value="atom">atom</option>\n+ <option value="nojump">nojump</option>\n+ <option value="cluster">cluster</option>\n+ <option value="whole">whole</option>\n+ </param>\n+ <param name="ur" type="select" label="Unit cell representation" >\n+ <option value="rect">rect</option>\n+ <option value="tric" selected="true">tric</option>\n+ <option value="zero">zero</option>\n+ </param>\n+ <param nam'..b'ment" >\n+ <option value="rect">rect</option>\n+ <option value="tric">tric</option>\n+ <option value="compact">compact</option>\n+ </param>\n+ </when>\n+ <when value="trjcat">\n+ <param name="trj_input" type="data" format=\'xtc,trr\' label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note this tool does not currently take order into account when concatenating." multiple="true"/>\n+ <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/>\n+ </when>\n+ </conditional>\n+ <param name="output_format" type="select" label="Output format" >\n+ <option value="xtc">XTC</option>\n+ <option value="trr">TRR</option>\n+ <option value="pdb">PDB</option>\n+ <option value="gro">GRO</option>\n+ </param>\n+ <section title="Time" name=\'time\' expanded="true">\n+ <param name="b" type="integer" label="Start time" help="Time (ps) of first frame to read from trajectory" value="0" min="0"/>\n+ <param name="e" type="integer" label="End time" help="Time (ps) of last frame to read from trajectory" value="-1" min="-1"/> <!-- stupidly this has different default values for trjconv and trjcat -->\n+ <param name="dt" type="integer" label="Write frames at this time interval (ps)" help="Only write frame when t is exactly divisible by this value. Leave as 0 to record all frames." value="0" min="0"/>\n+ </section>\n+ <expand macro="log" />\n+ </inputs>\n+ <outputs>\n+ <data name="output" format="xtc">\n+ <change_format>\n+ <when input="output_format" value="trr" format="trr"/>\n+ <when input="output_format" value="xtc" format="xtc"/>\n+ <when input="output_format" value="gro" format="dcd"/>\n+ <when input="output_format" value="pdb" format="pdb"/>\n+ </change_format>\n+ </data>\n+ </outputs> \n+ <tests>\n+ <test>\n+ <!-- gmx trjcat -f npt.xtc nvt.xtc -cat -o test.xtc -->\n+ <param name="trj_op" value="trjcat" />\n+ <param name="trj_input" value="npt.xtc,nvt.xtc" />\n+ <param name="b" value="0" />\n+ <param name="e" value="-1" />\n+ <param name="dt" value="0" />\n+ <param name="cat" value="true" />\n+ <output name="output" file="trjcat.xtc" ftype="xtc"/>\n+ </test>\n+ <test>\n+ <!-- echo \'1 1\' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -o npt_c.xtc -->\n+ <param name="trj_op" value="trjconv" />\n+ <param name="trj_input" value="npt.xtc" />\n+ <param name="str_input" value="npt.tpr" ftype="tpr"/>\n+ <param name="ndx_input" value="index.ndx" />\n+ <param name="b" value="0" />\n+ <param name="e" value="-1" />\n+ <param name="dt" value="0" />\n+ <param name="index_output" value="1" />\n+ <param name="index_center" value="1" />\n+ <param name="center" value="true" />\n+ <param name="pbc" value="mol" />\n+ <param name="ur" value="compact" />\n+ <param name="ur" value="tric" />\n+ <output name="output" file="trjconv.xtc" ftype="xtc"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+This tool allows manipulation of GROMACS trajectories, drawing on the trjcat and trjconv commands.\n+\n+_____\n+\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+ - One or more trajectory file (XTC or TRR)\n+ - Structure file (optional)\n+ - Various options can be set\n+\n+_____\n+\n+ \n+.. class:: infomark\n+\n+**Output**\n+\n+ - GROMACS trajectory or structure file (XTC, TRR, PDB, GRO)\n+\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |