| Previous changeset 8:4b4232c98b6e (2020-05-08) Next changeset 10:f197e34c33a9 (2020-10-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" |
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modified:
macros.xml sim.xml test-data/complex.gro test-data/complex.top test-data/index.ndx test-data/md.mdp test-data/minim.mdp test-data/newbox.gro test-data/npt.cpt test-data/npt.tpr test-data/npt.xtc test-data/nvt.xtc test-data/posre_cl.itp test-data/posres.itp test-data/processed.gro test-data/solv.gro test-data/topol.top test-data/topol_solv.top test-data/trjcat.xtc test-data/trjconv.xtc |
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added:
test-data/init.pdb test-data/newbox.pdb test-data/outp.edr test-data/outp.tabular test-data/outp.xvg test-data/str_ions.gro |
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removed:
test-data/1AKI.pdb test-data/em.edr test-data/em.gro test-data/em.tpr test-data/em.trr test-data/ions.mdp test-data/ions.tpr test-data/md_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.tabular 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/npt.edr test-data/npt.gro test-data/npt.mdp test-data/npt.pdb test-data/npt.trr 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/solv_ions.gro |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b macros.xml --- a/macros.xml Fri May 08 07:41:18 2020 -0400 +++ b/macros.xml Wed May 20 13:00:42 2020 -0400 |
| b |
| @@ -1,8 +1,8 @@ <macros> - <token name="@VERSION@">2019.1.5</token> + <token name="@TOOL_VERSION@">2020.2</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2019.1">gromacs</requirement> + <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement> </requirements> </xml> <xml name="citations"> |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b sim.xml --- a/sim.xml Fri May 08 07:41:18 2020 -0400 +++ b/sim.xml Wed May 20 13:00:42 2020 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool id="gmx_sim" name="GROMACS simulation" version="@VERSION@.1"> +<tool id="gmx_sim" name="GROMACS simulation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>for system equilibration or data collection</description> <macros> <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -43,8 +44,16 @@ -o outp.tpr &>> verbose.txt && - gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt - + gmx mdrun + -nt "\${GALAXY_SLOTS:-4}" + ## GPU + #if "\${GROMACS_GPU:-0}" == 1: + -ntmpi 1 + -nb gpu + -pme gpu + #end if + -deffnm outp &>> verbose.txt + #if $outps.str == 'pdb' or $outps.str == 'both' && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt #end if @@ -259,7 +268,7 @@ <tests> <test expect_num_outputs="3"> - <param name="gro_input" value="npt.gro" /> + <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <!-- <param name="cpt_bool" value="yes" /> --> <param name="cpt_in" value="npt.cpt" /> @@ -271,23 +280,27 @@ <param name="tpr_out" value="true"/> <param name="ensemble" value="npt" /> <!-- <param name="posres_bool" value="false" /> --> - <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> - <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> - <output name="output8" file="md_0_1.tpr" ftype="binary" compare="sim_size"/> - <!-- <output name="output1" ftype="gro"> + <output name="output1" ftype="gro"> <assert_contents> - <has_size value="2647999" /> + <has_size value="6537" /> + <has_n_lines n="97" /> + <has_line line="TEST in water" /> </assert_contents> </output> <output name="output3" ftype="trr"> <assert_contents> - <has_size value="10132584" /> + <has_size value="26136" /> </assert_contents> - </output> --> + </output> + <output name="output8" ftype="binary"> + <assert_contents> + <has_size value="44164" /> + </assert_contents> + </output> </test> <test expect_num_outputs="3"> - <param name="gro_input" value="npt.gro" /> + <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <!-- <param name="cpt_bool" value="yes" /> --> <param name="cpt_in" value="npt.cpt" /> @@ -297,13 +310,30 @@ <expand macro="test_params"/> <param name="ensemble" value="npt" /> <!-- <param name="posres_bool" value="false" /> --> - <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> - <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> - <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> + <output name="output1" ftype="gro"> + <assert_contents> + <has_size value="6537" /> + <has_n_lines n="97" /> + <has_line line="TEST in water" /> + </assert_contents> + </output> + <output name="output2" ftype="pdb"> + <assert_contents> + <has_size value="7582" /> + <has_n_lines n="100" /> + <has_line line="TITLE TEST in water" /> + <has_line line="REMARK THIS IS A SIMULATION BOX" /> + </assert_contents> + </output> + <output name="output3" ftype="trr"> + <assert_contents> + <has_size value="26136" /> + </assert_contents> + </output> </test> <test expect_num_outputs="3"> - <param name="gro_input" value="npt.gro" /> + <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <!-- <param name="cpt_bool" value="yes" /> --> <param name="cpt_in" value="npt.cpt" /> @@ -314,13 +344,30 @@ <expand macro="test_params"/> <param name="ensemble" value="npt" /> <!-- <param name="posres_bool" value="false" /> --> - <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> - <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> - <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> + <output name="output1" ftype="gro" compare="sim_size"> + <assert_contents> + <has_size value="6537" /> + <has_n_lines n="97" /> + <has_line line="TEST in water" /> + </assert_contents> + </output> + <output name="output2" ftype="pdb" compare="sim_size"> + <assert_contents> + <has_size value="7582" /> + <has_n_lines n="100" /> + <has_line line="TITLE TEST in water" /> + <has_line line="REMARK THIS IS A SIMULATION BOX" /> + </assert_contents> + </output> + <output name="output3" ftype="trr" compare="sim_size"> + <assert_contents> + <has_size value="26136" /> + </assert_contents> + </output> </test> <test expect_num_outputs="3"> - <param name="gro_input" value="em.gro" /> + <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <!-- <param name="posres_bool" value="true" /> --> <param name="itp_in" value="posres.itp" /> @@ -332,9 +379,24 @@ <param name="ensemble" value="nvt" /> <expand macro="test_params"/> - <output name="output2" file="nvt.pdb" ftype="pdb" compare="sim_size"/> - <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/> - <output name="output5" file="nvt.cpt" ftype="cpt" compare="sim_size"/> + <output name="output2" ftype="pdb"> + <assert_contents> + <has_size value="7582" /> + <has_n_lines n="100" /> + <has_line line="TITLE TEST in water" /> + <has_line line="REMARK THIS IS A SIMULATION BOX" /> + </assert_contents> + </output> + <output name="output4" ftype="xtc"> + <assert_contents> + <has_size value="4910" delta="20"/> + </assert_contents> + </output> + <output name="output5" ftype="cpt"> + <assert_contents> + <has_size value="3350" delta="20"/> + </assert_contents> + </output> </test> </tests> |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/1AKI.pdb --- a/test-data/1AKI.pdb Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1436 +0,0 @@\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 4b4232c98b6e -r a97dcfc23b4b test-data/complex.gro --- a/test-data/complex.gro Fri May 08 07:41:18 2020 -0400 +++ b/test-data/complex.gro Wed May 20 13:00:42 2020 -0400 |
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| b'@@ -1,2218 +1,116 @@\n GROningen MAchine for Chemical Simulation\n- 2215\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 '..b'15 1.652\n+ 2VAL HA 28 1.862 2.267 1.695\n+ 2VAL CB 29 1.859 2.118 1.562\n+ 2VAL HB 30 1.931 2.067 1.515\n+ 2VAL CG1 31 1.770 2.023 1.642\n+ 2VAL HG11 32 1.722 1.962 1.579\n+ 2VAL HG12 33 1.827 1.970 1.704\n+ 2VAL HG13 34 1.703 2.076 1.694\n+ 2VAL CG2 35 1.774 2.186 1.456\n+ 2VAL HG21 36 1.728 2.117 1.401\n+ 2VAL HG22 37 1.707 2.245 1.500\n+ 2VAL HG23 38 1.833 2.242 1.397\n+ 2VAL C 39 2.025 2.146 1.756\n+ 2VAL O 40 2.121 2.076 1.719\n+ 3PHE N 41 1.994 2.170 1.881\n+ 3PHE H 42 1.920 2.234 1.901\n+ 3PHE CA 43 2.064 2.105 1.993\n+ 3PHE HA 44 2.160 2.112 1.968\n+ 3PHE CB 45 2.042 2.178 2.126\n+ 3PHE HB1 46 1.950 2.217 2.127\n+ 3PHE HB2 47 2.051 2.113 2.201\n+ 3PHE CG 48 2.139 2.289 2.147\n+ 3PHE CD1 49 2.112 2.420 2.105\n+ 3PHE HD1 50 2.026 2.440 2.058\n+ 3PHE CD2 51 2.245 2.271 2.238\n+ 3PHE HD2 52 2.258 2.181 2.280\n+ 3PHE CE1 53 2.203 2.523 2.128\n+ 3PHE HE1 54 2.193 2.610 2.081\n+ 3PHE CE2 55 2.332 2.374 2.269\n+ 3PHE HE2 56 2.411 2.357 2.328\n+ 3PHE CZ 57 2.309 2.502 2.218\n+ 3PHE HZ 58 2.367 2.579 2.246\n+ 3PHE C 59 2.019 1.959 2.008\n+ 3PHE O 60 1.897 1.931 1.999\n+ 4GLY N 61 2.117 1.879 2.052\n+ 4GLY H 62 2.212 1.910 2.053\n+ 4GLY CA 63 2.082 1.743 2.098\n+ 4GLY HA1 64 2.007 1.707 2.042\n+ 4GLY HA2 65 2.161 1.683 2.091\n+ 4GLY C 66 2.037 1.757 2.243\n+ 4GLY O 67 2.075 1.855 2.307\n+ 5ARG N 68 1.950 1.669 2.288\n+ 5ARG H 69 1.916 1.599 2.225\n+ 5ARG CA 70 1.901 1.669 2.426\n+ 5ARG HA 71 1.843 1.749 2.433\n+ 5ARG CB 72 1.821 1.541 2.452\n+ 5ARG HB1 73 1.745 1.537 2.388\n+ 5ARG HB2 74 1.881 1.462 2.438\n+ 5ARG CG 75 1.766 1.535 2.593\n+ 5ARG HG1 76 1.842 1.532 2.658\n+ 5ARG HG2 77 1.710 1.616 2.610\n+ 5ARG CD 78 1.683 1.415 2.613\n+ 5ARG HD1 79 1.649 1.414 2.707\n+ 5ARG HD2 80 1.605 1.420 2.550\n+ 5ARG NE 81 1.751 1.290 2.589\n+ 5ARG HE 82 1.747 1.255 2.496\n+ 5ARG CZ 83 1.818 1.216 2.675\n+ 5ARG NH1 84 1.829 1.248 2.804\n+ 5ARG HH11 85 1.784 1.331 2.838\n+ 5ARG HH12 86 1.881 1.190 2.866\n+ 5ARG NH2 87 1.870 1.099 2.632\n+ 5ARG HH21 88 1.856 1.070 2.538\n+ 5ARG HH22 89 1.921 1.041 2.695\n+ 5ARG C 90 2.012 1.688 2.529\n+ 5ARG O1 91 2.012 1.780 2.615\n+ 5ARG O2 92 1.975 1.689 2.660\n+ 6G5E C1 93 6.456 3.250 2.707\n+ 6G5E C2 94 6.330 3.283 2.656\n+ 6G5E C3 95 6.321 3.361 2.541\n+ 6G5E C7 96 6.426 3.498 2.362\n+ 6G5E C10 97 6.449 3.677 2.236\n+ 6G5E C12 98 6.570 3.684 2.448\n+ 6G5E C13 99 6.707 3.692 2.422\n+ 6G5E C14 100 6.793 3.751 2.516\n+ 6G5E C15 101 6.742 3.801 2.635\n+ 6G5E C16 102 6.605 3.793 2.661\n+ 6G5E C4 103 6.438 3.406 2.478\n+ 6G5E C5 104 6.564 3.375 2.531\n+ 6G5E C6 105 6.572 3.297 2.645\n+ 6G5E N8 106 6.353 3.478 2.256\n+ 6G5E N9 107 6.368 3.590 2.173\n+ 6G5E N11 108 6.485 3.623 2.353\n+ 6G5E C17 109 6.519 3.734 2.568\n+ 6G5E S18 110 6.498 3.829 2.176\n+ 6G5E F19 111 6.755 3.642 2.306\n+ 6G5E O20 112 6.199 3.392 2.489\n+ 6G5E O21 113 6.465 3.175 2.819\n+ 4.09123 4.09123 4.09123\n' |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/complex.top --- a/test-data/complex.top Fri May 08 07:41:18 2020 -0400 +++ b/test-data/complex.top Wed May 20 13:00:42 2020 -0400 |
| [ |
| b"@@ -2,18 +2,18 @@\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+;\tAt date: Tue May 12 12:59:21 2020\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+;\tExecutable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/__gromacs@2019.1\n+;\tWorking dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working\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+;\t gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all\n ;\tForce field was read from the standard GROMACS share directory.\n ;\n \n@@ -36,7 +36,7 @@\n \n [ moleculetype ]\n ; Name nrexcl\n-Protein_chain_A 3\n+Protein 3\n \n [ atoms ]\n ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n@@ -111,10 +111,10 @@\n 65 opls_140 4 GLY HA2 21 0.06 1.008\n 66 opls_235 4 GLY C 22 0.5 12.011\n 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2\n-; residue 5 ARG rtp ARG q +1.0\n+; residue 5 ARG rtp ARG q 0.0\n 68 opls_238 5 ARG N 23 -0.5 14.0067\n 69 opls_241 5 ARG H 23 0.3 1.008\n- 70 opls_224B 5 ARG CA 23 0.14 12.011\n+ 70 opls_283 5 ARG CA 23 0.04 12.011\n 71 opls_140 5 ARG HA 23 0.06 1.008\n 72 opls_136 5 ARG CB 24 -0.12 12.011\n 73 opls_140 5 ARG HB1 24 0.06 1.008\n@@ -134,2001 +134,9 @@\n 87 opls_300 5 ARG NH2 29 -0.8 14.0067\n 88 opls_301 5 ARG HH21 29 0.46 1.008\n 89 opls_301 5 ARG HH22 29 0.46 1.008\n- 90 opls_235 5 ARG C 30 0.5 12.011\n- 91 opls_236 5 ARG O 30 -0.5 15.9994 ; qtot 3\n-; residue 6 CYS rtp CYS2 q 0.0\n- 92 opls_238 6 CYS N 31 -0.5 14.0067\n- 93 opls_241 6 CYS H 31 0.3 1.008\n- 94 opls_224B 6 CYS CA 31 0.14 12.011\n- 95 opls_140 6 CYS HA 31 0.06 1.008\n- 96 opls_214 6 CYS CB 32 0.0975 12.011\n- 97 opls_140 6 CYS HB1 32 0.06 1.008\n- 98 opls_140 6 CYS HB2 32 0.06 1.008\n- 99 opls_203 6 CYS SG 32 -0.2175 32.06\n- 100 opls_235 6 CYS C 33 0.5 12.011\n- 101 opls_236 6 CYS O 33 -0.5 15.9994 ; qtot 3\n-; residue 7 GLU rtp GLU q -1.0\n- 102 opls_238 7 GLU N 34 -0.5 14.0067\n- 103 opls_241 7 GLU H 34 0.3 1.008\n- 104 opls_224B 7 GLU CA 34 0.14 12.011\n- 105 opls_140 7 GLU HA 34 0.06 1.008\n- 106 opls_136 7 GLU CB 35 -0.12 12.011\n- 107 opls_140 7 GLU HB1 35 0.06 1.008\n- 108 opls_140 7 GLU HB2 35 0.06 1.008\n- 109 opls_274 7 GLU CG 36 -0.22 12.011\n- 110 opls_140 7 GLU HG1 36 0.06 1.008\n- 111 opls_140 7 GLU HG2 36 0.06 1.008\n- 112 opls_271 7 GLU CD 37 0.7 12.011\n- 113 opls_272 7 GLU OE1 37 -0.8 15.999"..b' 1 improper_O_C_X_Y\n- 1637 1641 1639 1640 1 improper_Z_N_X_Y\n- 1641 1663 1661 1662 1 improper_O_C_X_Y\n- 1643 1646 1649 1647 1 improper_Z_CA_X_Y\n- 1646 1650 1647 1648 1 improper_Z_CA_X_Y\n- 1647 1652 1650 1651 1 improper_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@@ -18606,10 +1107,9 @@\n \n [ system ]\n ; Name\n-LYSOZYME\n+TEST\n \n [ molecules ]\n ; Compound #mols\n-Protein_chain_A 1\n-SOL 78\n+Protein 1\n base 1\n' |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/em.edr |
| b |
| Binary file test-data/em.edr has changed |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/em.gro --- a/test-data/em.gro Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,38379 +0,0 @@\n-LYSOZYME in water\n-38376\n- 1LYS N 1 4.422 3.406 2.462\n- 1LYS H1 2 4.494 3.461 2.416\n- 1LYS H2 3 4.354 3.379 2.393\n- 1LYS H3 4 4.377 3.460 2.536\n- 1LYS CA 5 4.475 3.284 2.524\n- 1LYS HA 6 4.525 3.225 2.448\n- 1LYS CB 7 4.578 3.317 2.635\n- 1LYS HB1 8 4.664 3.365 2.589\n- 1LYS HB2 9 4.537 3.390 2.705\n- 1LYS CG 10 4.627 3.195 2.715\n- 1LYS HG1 11 4.550 3.164 2.786\n- 1LYS HG2 12 4.640 3.112 2.647\n- 1LYS CD 13 4.759 3.218 2.790\n- 1LYS HD1 14 4.838 3.237 2.718\n- 1LYS HD2 15 4.751 3.306 2.854\n- 1LYS CE 16 4.795 3.094 2.875\n- 1LYS HE1 17 4.726 3.085 2.959\n- 1LYS HE2 18 4.785 3.003 2.817\n- 1LYS NZ 19 4.932 3.099 2.926\n- 1LYS HZ1 20 4.942 3.016 2.986\n- 1LYS HZ2 21 4.998 3.088 2.850\n- 1LYS HZ3 22 4.950 3.185 2.977\n- 1LYS C 23 4.358 3.203 2.578\n- 1LYS O 24 4.272 3.260 2.645\n- 2VAL N 25 4.356 3.072 2.555\n- 2VAL H 26 4.430 3.030 2.497\n- 2VAL CA 27 4.277 2.978 2.633\n- 2VAL HA 28 4.200 3.028 2.690\n- 2VAL CB 29 4.210 2.872 2.542\n- 2VAL HB 30 4.288 2.814 2.492\n- 2VAL CG1 31 4.121 2.775 2.623\n- 2VAL HG11 32 4.069 2.705 2.558\n- 2VAL HG12 33 4.179 2.716 2.694\n- 2VAL HG13 34 4.045 2.829 2.680\n- 2VAL CG2 35 4.125 2.937 2.432\n- 2VAL HG21 36 4.075 2.863 2.371\n- 2VAL HG22 37 4.049 3.000 2.477\n- 2VAL HG23 38 4.185 3.000 2.365\n- 2VAL C 39 4.378 2.913 2.729\n- 2VAL O 40 4.480 2.858 2.686\n- 3PHE N 41 4.350 2.923 2.858\n- 3PHE H 42 4.262 2.968 2.884\n- 3PHE CA 43 4.425 2.856 2.964\n- 3PHE HA 44 4.532 2.858 2.942\n- 3PHE CB 45 4.396 2.927 3.098\n- 3PHE HB1 46 4.294 2.964 3.103\n- 3PHE HB2 47 4.405 2.855 3.179\n- 3PHE CG 48 4.489 3.043 3.132\n- 3PHE CD1 49 4.468 3.171 3.079\n- 3PHE HD1 50 4.385 3.188 3.012\n- 3PHE CD2 51 4.595 3.021 3.221\n- 3PHE HD2 52 4.609 2.923 3.263\n- 3PHE CE1 53 4.556 3.276 3.112\n- 3PHE HE1 54 4.541 3.375 3.072\n- 3PHE CE2 55 4.683 3.126 3.256\n- 3PHE HE2 56 4.764 3.108 3.324\n- 3PHE CZ 57 4.663 3.254 3.200\n- 3PHE HZ 58 4.730 3.335 3.226\n- 3PHE C 59 4.376 2.711 2.977\n- 3PHE O 60 4.258 2.680 2.956\n- 4GLY N 61 4.465 2.625 3.025\n- 4GLY H 62 4.562 2.656 3.035\n- 4GLY CA 63 4.428 2.493 3.075\n- 4GLY HA1 64 4.346 2.449 3.018\n- 4GLY HA2 65 4.514 2.427 3.064\n- 4GLY C 66 4.392 2.506 3.224\n- 4GLY O 67 4.443 2.595 3.292\n- 5ARG N 68 4.303 2.419 3.275\n- 5ARG H 69 4.261 2.352 3.212\n- 5ARG CA 70 4.249 2.422 3.412\n- 5ARG HA 71 4.184 2.510 3.417\n- 5ARG CB 72 4.163 2.296 3.436\n- 5ARG HB1 73 4.079 2.296 3.367\n- 5ARG HB2 74 4.221 2.208 3.410\n- 5ARG CG 75 4.109 2.279 3.579\n- 5ARG HG1 76 4.190 2.273 3.651\n- 5ARG HG2 77 4.051 2.367 3.607\n- 5ARG CD 78 4.021 2.154 3.596\n- 5ARG HD1 79 3.975 2.151 3.694\n- 5ARG HD2 80 3.938 2.157 3.525\n- 5ARG NE 81 4.096 2.030 3.574\n- 5ARG HE 82 4.077 1.988 3.482\n- 5ARG CZ 83 4.166 1.961 3.666\n- 5ARG NH1 84 4.183 2.007 3.790\n- 5ARG HH11 85 4.151 2.100 3.820\n- 5ARG HH12 86 4.226 1.946 3.8'..b'24 5.807\n-12240SOL OW38291 6.209 6.418 7.023\n-12240SOL HW138292 6.268 6.497 7.006\n-12240SOL HW238293 6.264 6.336 7.032\n-12241SOL OW38294 7.074 7.332 6.559\n-12241SOL HW138295 7.101 0.064 6.495\n-12241SOL HW238296 7.152 7.306 6.615\n-12242SOL OW38297 6.297 6.153 7.291\n-12242SOL HW138298 6.340 6.230 7.339\n-12242SOL HW238299 6.350 6.070 7.309\n-12243SOL OW38300 5.975 7.307 7.149\n-12243SOL HW138301 5.904 0.039 7.142\n-12243SOL HW238302 5.938 7.228 7.199\n-12244SOL OW38303 7.272 6.459 6.820\n-12244SOL HW138304 7.260 6.373 6.771\n-12244SOL HW238305 7.241 6.535 6.762\n-12245SOL OW38306 6.830 5.912 6.034\n-12245SOL HW138307 6.887 5.829 6.032\n-12245SOL HW238308 6.847 5.961 6.119\n-12246SOL OW38309 6.173 6.323 6.254\n-12246SOL HW138310 6.215 6.413 6.242\n-12246SOL HW238311 6.103 6.310 6.184\n-12247SOL OW38312 7.302 6.503 7.086\n-12247SOL HW138313 7.339 6.594 7.103\n-12247SOL HW238314 7.302 6.484 6.988\n-12248SOL OW38315 6.439 6.955 5.624\n-12248SOL HW138316 6.408 6.972 5.718\n-12248SOL HW238317 6.471 7.040 5.583\n-12249SOL OW38318 6.454 6.556 6.442\n-12249SOL HW138319 6.506 6.478 6.478\n-12249SOL HW238320 6.413 6.607 6.517\n-12250SOL OW38321 6.663 6.579 5.671\n-12250SOL HW138322 6.637 6.629 5.588\n-12250SOL HW238323 6.741 6.519 5.650\n-12251SOL OW38324 0.053 7.124 6.435\n-12251SOL HW138325 7.317 7.105 6.372\n-12251SOL HW238326 0.079 7.039 6.481\n-12252SOL OW38327 5.680 6.816 6.247\n-12252SOL HW138328 5.679 6.773 6.337\n-12252SOL HW238329 5.745 6.769 6.187\n-12253SOL OW38330 6.263 6.982 7.212\n-12253SOL HW138331 6.190 6.923 7.247\n-12253SOL HW238332 6.257 7.072 7.255\n-12254SOL OW38333 7.331 5.751 6.842\n-12254SOL HW138334 0.046 5.667 6.850\n-12254SOL HW238335 0.006 5.793 6.752\n-12255SOL OW38336 6.014 6.018 6.110\n-12255SOL HW138337 6.052 5.951 6.047\n-12255SOL HW238338 5.965 5.971 6.184\n-12256SOL OW38339 5.916 6.142 6.875\n-12256SOL HW138340 5.974 6.086 6.934\n-12256SOL HW238341 5.932 6.117 6.779\n-12257SOL OW38342 6.428 7.138 6.264\n-12257SOL HW138343 6.414 7.218 6.207\n-12257SOL HW238344 6.342 7.086 6.270\n-12258SOL OW38345 7.019 5.813 6.706\n-12258SOL HW138346 7.051 5.727 6.747\n-12258SOL HW238347 6.963 5.862 6.774\n-12259SOL OW38348 6.595 5.600 6.726\n-12259SOL HW138349 6.534 5.541 6.673\n-12259SOL HW238350 6.686 5.561 6.728\n-12260SOL OW38351 6.363 6.915 5.901\n-12260SOL HW138352 6.333 6.821 5.913\n-12260SOL HW238353 6.444 6.932 5.958\n-12261SOL OW38354 6.211 7.150 6.873\n-12261SOL HW138355 6.213 7.218 6.947\n-12261SOL HW238356 6.302 7.142 6.833\n-12262SOL OW38357 6.949 5.635 5.749\n-12262SOL HW138358 6.988 5.565 5.689\n-12262SOL HW238359 6.855 5.609 5.774\n-12263SOL OW38360 6.874 6.047 6.269\n-12263SOL HW138361 6.819 6.131 6.269\n-12263SOL HW238362 6.871 6.006 6.360\n-12264SOL OW38363 7.183 5.810 6.483\n-12264SOL HW138364 7.125 5.800 6.564\n-12264SOL HW238365 7.144 5.878 6.422\n-12265SOL OW38366 5.630 6.651 5.892\n-12265SOL HW138367 5.728 6.649 5.873\n-12265SOL HW238368 5.599 6.558 5.915\n-12266CL CL38369 0.201 2.832 1.237\n-12267CL CL38370 1.614 2.267 3.255\n-12268CL CL38371 1.597 7.226 3.986\n-12269CL CL38372 1.368 6.406 5.944\n-12270CL CL38373 3.098 3.643 6.186\n-12271CL CL38374 2.871 3.928 1.863\n-12272CL CL38375 7.226 0.967 0.588\n-12273CL CL38376 6.448 5.573 6.100\n- 7.33925 7.33925 7.33925\n' |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/em.tpr |
| b |
| Binary file test-data/em.tpr has changed |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/em.trr |
| b |
| Binary file test-data/em.trr has changed |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/index.ndx --- a/test-data/index.ndx Fri May 08 07:41:18 2020 -0400 +++ b/test-data/index.ndx Wed May 20 13:00:42 2020 -0400 |
| b |
| b'@@ -5,2559 +5,7 @@\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 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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+ 93 94\n' |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/init.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/init.pdb Wed May 20 13:00:42 2020 -0400 |
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| @@ -0,0 +1,97 @@ +TITLE TEST +REMARK THIS IS A SIMULATION BOX +CRYST1 59.062 68.451 30.517 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 N LYS 1 35.360 22.340 -11.980 1.00 0.00 +ATOM 2 H1 LYS 1 36.120 22.880 -12.360 1.00 0.00 +ATOM 3 H2 LYS 1 34.700 22.140 -12.700 1.00 0.00 +ATOM 4 H3 LYS 1 34.920 22.860 -11.250 1.00 0.00 +ATOM 5 CA LYS 1 35.890 21.070 -11.430 1.00 0.00 +ATOM 6 HA LYS 1 36.330 20.550 -12.160 1.00 0.00 +ATOM 7 CB LYS 1 36.870 21.440 -10.310 1.00 0.00 +ATOM 8 HB1 LYS 1 37.630 21.950 -10.700 1.00 0.00 +ATOM 9 HB2 LYS 1 36.390 22.010 -9.640 1.00 0.00 +ATOM 10 CG LYS 1 37.450 20.250 -9.560 1.00 0.00 +ATOM 11 HG1 LYS 1 36.760 19.890 -8.940 1.00 0.00 +ATOM 12 HG2 LYS 1 37.700 19.540 -10.230 1.00 0.00 +ATOM 13 CD LYS 1 38.690 20.650 -8.770 1.00 0.00 +ATOM 14 HD1 LYS 1 39.450 20.830 -9.400 1.00 0.00 +ATOM 15 HD2 LYS 1 38.490 21.470 -8.240 1.00 0.00 +ATOM 16 CE LYS 1 39.060 19.510 -7.840 1.00 0.00 +ATOM 17 HE1 LYS 1 38.410 19.460 -7.080 1.00 0.00 +ATOM 18 HE2 LYS 1 39.060 18.640 -8.330 1.00 0.00 +ATOM 19 NZ LYS 1 40.420 19.770 -7.300 1.00 0.00 +ATOM 20 HZ1 LYS 1 40.690 19.030 -6.680 1.00 0.00 +ATOM 21 HZ2 LYS 1 41.080 19.820 -8.060 1.00 0.00 +ATOM 22 HZ3 LYS 1 40.420 20.640 -6.800 1.00 0.00 +ATOM 23 C LYS 1 34.740 20.260 -10.840 1.00 0.00 +ATOM 24 O LYS 1 33.950 20.810 -10.080 1.00 0.00 +ATOM 25 N VAL 2 34.740 18.960 -11.040 1.00 0.00 +ATOM 26 H VAL 2 35.360 18.600 -11.740 1.00 0.00 +ATOM 27 CA VAL 2 33.900 18.000 -10.330 1.00 0.00 +ATOM 28 HA VAL 2 33.170 18.520 -9.900 1.00 0.00 +ATOM 29 CB VAL 2 33.140 17.030 -11.230 1.00 0.00 +ATOM 30 HB VAL 2 33.860 16.520 -11.700 1.00 0.00 +ATOM 31 CG1 VAL 2 32.250 16.080 -10.430 1.00 0.00 +ATOM 32 1HG1 VAL 2 31.770 15.470 -11.060 1.00 0.00 +ATOM 33 2HG1 VAL 2 32.820 15.550 -9.810 1.00 0.00 +ATOM 34 3HG1 VAL 2 31.580 16.610 -9.910 1.00 0.00 +ATOM 35 CG2 VAL 2 32.290 17.710 -12.290 1.00 0.00 +ATOM 36 1HG2 VAL 2 31.830 17.020 -12.840 1.00 0.00 +ATOM 37 2HG2 VAL 2 31.620 18.300 -11.850 1.00 0.00 +ATOM 38 3HG2 VAL 2 32.880 18.270 -12.880 1.00 0.00 +ATOM 39 C VAL 2 34.800 17.310 -9.290 1.00 0.00 +ATOM 40 O VAL 2 35.760 16.610 -9.660 1.00 0.00 +ATOM 41 N PHE 3 34.490 17.550 -8.040 1.00 0.00 +ATOM 42 H PHE 3 33.750 18.190 -7.840 1.00 0.00 +ATOM 43 CA PHE 3 35.190 16.900 -6.920 1.00 0.00 +ATOM 44 HA PHE 3 36.150 16.970 -7.170 1.00 0.00 +ATOM 45 CB PHE 3 34.970 17.630 -5.590 1.00 0.00 +ATOM 46 HB1 PHE 3 34.050 18.020 -5.580 1.00 0.00 +ATOM 47 HB2 PHE 3 35.060 16.980 -4.840 1.00 0.00 +ATOM 48 CG PHE 3 35.940 18.740 -5.380 1.00 0.00 +ATOM 49 CD1 PHE 3 35.670 20.050 -5.800 1.00 0.00 +ATOM 50 HD1 PHE 3 34.810 20.250 -6.270 1.00 0.00 +ATOM 51 CD2 PHE 3 37.000 18.560 -4.470 1.00 0.00 +ATOM 52 HD2 PHE 3 37.130 17.660 -4.050 1.00 0.00 +ATOM 53 CE1 PHE 3 36.580 21.080 -5.570 1.00 0.00 +ATOM 54 HE1 PHE 3 36.480 21.950 -6.040 1.00 0.00 +ATOM 55 CE2 PHE 3 37.870 19.590 -4.160 1.00 0.00 +ATOM 56 HE2 PHE 3 38.660 19.420 -3.570 1.00 0.00 +ATOM 57 CZ PHE 3 37.640 20.870 -4.670 1.00 0.00 +ATOM 58 HZ PHE 3 38.220 21.640 -4.390 1.00 0.00 +ATOM 59 C PHE 3 34.740 15.440 -6.770 1.00 0.00 +ATOM 60 O PHE 3 33.520 15.160 -6.860 1.00 0.00 +ATOM 61 N GLY 4 35.720 14.640 -6.330 1.00 0.00 +ATOM 62 H GLY 4 36.670 14.950 -6.320 1.00 0.00 +ATOM 63 CA GLY 4 35.370 13.280 -5.870 1.00 0.00 +ATOM 64 HA1 GLY 4 34.620 12.920 -6.430 1.00 0.00 +ATOM 65 HA2 GLY 4 36.160 12.680 -5.940 1.00 0.00 +ATOM 66 C GLY 4 34.920 13.420 -4.420 1.00 0.00 +ATOM 67 O GLY 4 35.300 14.400 -3.780 1.00 0.00 +ATOM 68 N ARG 5 34.050 12.540 -3.970 1.00 0.00 +ATOM 69 H ARG 5 33.710 11.840 -4.600 1.00 0.00 +ATOM 70 CA ARG 5 33.560 12.540 -2.590 1.00 0.00 +ATOM 71 HA ARG 5 32.980 13.340 -2.520 1.00 0.00 +ATOM 72 CB ARG 5 32.760 11.260 -2.330 1.00 0.00 +ATOM 73 HB1 ARG 5 32.000 11.220 -2.970 1.00 0.00 +ATOM 74 HB2 ARG 5 33.360 10.470 -2.470 1.00 0.00 +ATOM 75 CG ARG 5 32.210 11.200 -0.920 1.00 0.00 +ATOM 76 HG1 ARG 5 32.970 11.170 -0.270 1.00 0.00 +ATOM 77 HG2 ARG 5 31.650 12.010 -0.750 1.00 0.00 +ATOM 78 CD ARG 5 31.380 10.000 -0.720 1.00 0.00 +ATOM 79 HD1 ARG 5 31.040 9.990 0.220 1.00 0.00 +ATOM 80 HD2 ARG 5 30.600 10.050 -1.350 1.00 0.00 +ATOM 81 NE ARG 5 32.060 8.750 -0.960 1.00 0.00 +ATOM 82 HE ARG 5 32.020 8.400 -1.890 1.00 0.00 +ATOM 83 CZ ARG 5 32.730 8.010 -0.100 1.00 0.00 +ATOM 84 NH1 ARG 5 32.840 8.330 1.190 1.00 0.00 +ATOM 85 1HH1 ARG 5 32.390 9.160 1.530 1.00 0.00 +ATOM 86 2HH1 ARG 5 33.360 7.750 1.810 1.00 0.00 +ATOM 87 NH2 ARG 5 33.250 6.840 -0.530 1.00 0.00 +ATOM 88 1HH2 ARG 5 33.110 6.550 -1.470 1.00 0.00 +ATOM 89 2HH2 ARG 5 33.760 6.260 0.100 1.00 0.00 +ATOM 90 C ARG 5 34.670 12.730 -1.560 1.00 0.00 +ATOM 91 O ARG 5 34.670 13.650 -0.700 1.00 0.00 +TER +ENDMDL |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/ions.mdp --- a/test-data/ions.mdp Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,15 +0,0 @@ -; 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) |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/ions.tpr |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/md.mdp --- a/test-data/md.mdp Fri May 08 07:41:18 2020 -0400 +++ b/test-data/md.mdp Wed May 20 13:00:42 2020 -0400 |
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| @@ -1,46 +1,50 @@ -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 + + 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 ; group(s) to write to the compressed trajectory file + ; 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 cut-off + rlist = 1.0 ; Cut-off distance for the short-range neighbor list. + rvdw = 1.0 ; Short-range Van der Waals cut-off + ; Electrostatics + coulombtype = PME ; method for electrostatics calculations e.g. PME + 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 + ; 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 + ; 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 + + \ No newline at end of file |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.cpt |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.edr |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.gro --- a/test-data/md_0_1.gro Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,38379 +0,0 @@\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 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.ndx --- a/test-data/md_0_1.ndx Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,13032 +0,0 @@\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 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.pdb --- a/test-data/md_0_1.pdb Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,38382 +0,0 @@\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 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.tabular --- a/test-data/md_0_1.tabular Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -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 |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.tpr |
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| Binary file test-data/md_0_1.tpr has changed |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.trr |
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| Binary file test-data/md_0_1.trr has changed |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.xtc |
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| Binary file test-data/md_0_1.xtc has changed |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/md_0_1.xvg --- a/test-data/md_0_1.xvg Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,37 +0,0 @@ -# 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 4b4232c98b6e -r a97dcfc23b4b test-data/minim.mdp --- a/test-data/minim.mdp Fri May 08 07:41:18 2020 -0400 +++ b/test-data/minim.mdp Wed May 20 13:00:42 2020 -0400 |
| b |
| @@ -1,14 +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 +integrator = steep ; Algorithm (steep = steepest descent minimization) +emtol = 1000.0 ; Stop minimization when the maximum force is less than this value emstep = 0.01 ; Energy step size -nsteps = 50000 ; Maximum number of (minimization) steps to perform - +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 +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) +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 +rlist = 1.0 ; Cut-off distance for the short-range neighbor list. +rvdw = 1.0 ; Short-range Van der Waals cut-off +pbc = xyz ; Periodic Boundary Conditions (yes/no) \ No newline at end of file |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/newbox.gro --- a/test-data/newbox.gro Fri May 08 07:41:18 2020 -0400 +++ b/test-data/newbox.gro Wed May 20 13:00:42 2020 -0400 |
| b |
| b'@@ -1,2197 +1,95 @@\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- 5'..b'70 1.469\n+ 1LYS CB 7 2.232 2.559 1.654\n+ 1LYS HB1 8 2.308 2.610 1.615\n+ 1LYS HB2 9 2.184 2.616 1.721\n+ 1LYS CG 10 2.290 2.440 1.729\n+ 1LYS HG1 11 2.221 2.404 1.791\n+ 1LYS HG2 12 2.315 2.369 1.662\n+ 1LYS CD 13 2.414 2.480 1.808\n+ 1LYS HD1 14 2.490 2.498 1.745\n+ 1LYS HD2 15 2.394 2.562 1.861\n+ 1LYS CE 16 2.451 2.366 1.901\n+ 1LYS HE1 17 2.386 2.361 1.977\n+ 1LYS HE2 18 2.451 2.279 1.852\n+ 1LYS NZ 19 2.587 2.392 1.955\n+ 1LYS HZ1 20 2.614 2.318 2.017\n+ 1LYS HZ2 21 2.653 2.397 1.879\n+ 1LYS HZ3 22 2.587 2.479 2.005\n+ 1LYS C 23 2.019 2.441 1.601\n+ 1LYS O 24 1.940 2.496 1.677\n+ 2VAL N 25 2.019 2.311 1.581\n+ 2VAL H 26 2.081 2.275 1.511\n+ 2VAL CA 27 1.935 2.215 1.652\n+ 2VAL HA 28 1.862 2.267 1.695\n+ 2VAL CB 29 1.859 2.118 1.562\n+ 2VAL HB 30 1.931 2.067 1.515\n+ 2VAL CG1 31 1.770 2.023 1.642\n+ 2VAL HG11 32 1.722 1.962 1.579\n+ 2VAL HG12 33 1.827 1.970 1.704\n+ 2VAL HG13 34 1.703 2.076 1.694\n+ 2VAL CG2 35 1.774 2.186 1.456\n+ 2VAL HG21 36 1.728 2.117 1.401\n+ 2VAL HG22 37 1.707 2.245 1.500\n+ 2VAL HG23 38 1.833 2.242 1.397\n+ 2VAL C 39 2.025 2.146 1.756\n+ 2VAL O 40 2.121 2.076 1.719\n+ 3PHE N 41 1.994 2.170 1.881\n+ 3PHE H 42 1.920 2.234 1.901\n+ 3PHE CA 43 2.064 2.105 1.993\n+ 3PHE HA 44 2.160 2.112 1.968\n+ 3PHE CB 45 2.042 2.178 2.126\n+ 3PHE HB1 46 1.950 2.217 2.127\n+ 3PHE HB2 47 2.051 2.113 2.201\n+ 3PHE CG 48 2.139 2.289 2.147\n+ 3PHE CD1 49 2.112 2.420 2.105\n+ 3PHE HD1 50 2.026 2.440 2.058\n+ 3PHE CD2 51 2.245 2.271 2.238\n+ 3PHE HD2 52 2.258 2.181 2.280\n+ 3PHE CE1 53 2.203 2.523 2.128\n+ 3PHE HE1 54 2.193 2.610 2.081\n+ 3PHE CE2 55 2.332 2.374 2.269\n+ 3PHE HE2 56 2.411 2.357 2.328\n+ 3PHE CZ 57 2.309 2.502 2.218\n+ 3PHE HZ 58 2.367 2.579 2.246\n+ 3PHE C 59 2.019 1.959 2.008\n+ 3PHE O 60 1.897 1.931 1.999\n+ 4GLY N 61 2.117 1.879 2.052\n+ 4GLY H 62 2.212 1.910 2.053\n+ 4GLY CA 63 2.082 1.743 2.098\n+ 4GLY HA1 64 2.007 1.707 2.042\n+ 4GLY HA2 65 2.161 1.683 2.091\n+ 4GLY C 66 2.037 1.757 2.243\n+ 4GLY O 67 2.075 1.855 2.307\n+ 5ARG N 68 1.950 1.669 2.288\n+ 5ARG H 69 1.916 1.599 2.225\n+ 5ARG CA 70 1.901 1.669 2.426\n+ 5ARG HA 71 1.843 1.749 2.433\n+ 5ARG CB 72 1.821 1.541 2.452\n+ 5ARG HB1 73 1.745 1.537 2.388\n+ 5ARG HB2 74 1.881 1.462 2.438\n+ 5ARG CG 75 1.766 1.535 2.593\n+ 5ARG HG1 76 1.842 1.532 2.658\n+ 5ARG HG2 77 1.710 1.616 2.610\n+ 5ARG CD 78 1.683 1.415 2.613\n+ 5ARG HD1 79 1.649 1.414 2.707\n+ 5ARG HD2 80 1.605 1.420 2.550\n+ 5ARG NE 81 1.751 1.290 2.589\n+ 5ARG HE 82 1.747 1.255 2.496\n+ 5ARG CZ 83 1.818 1.216 2.675\n+ 5ARG NH1 84 1.829 1.248 2.804\n+ 5ARG HH11 85 1.784 1.331 2.838\n+ 5ARG HH12 86 1.881 1.190 2.866\n+ 5ARG NH2 87 1.870 1.099 2.632\n+ 5ARG HH21 88 1.856 1.070 2.538\n+ 5ARG HH22 89 1.921 1.041 2.695\n+ 5ARG C 90 2.012 1.688 2.529\n+ 5ARG O1 91 2.012 1.780 2.615\n+ 5ARG O2 92 1.975 1.689 2.660\n+ 4.09123 4.09123 4.09123\n' |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/newbox.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/newbox.pdb Wed May 20 13:00:42 2020 -0400 |
| b |
| @@ -0,0 +1,98 @@ +TITLE TEST +REMARK THIS IS A SIMULATION BOX +CRYST1 40.912 40.912 40.912 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 N LYS 1 20.810 26.490 14.870 1.00 0.00 +ATOM 2 H1 LYS 1 21.570 27.030 14.490 1.00 0.00 +ATOM 3 H2 LYS 1 20.150 26.290 14.150 1.00 0.00 +ATOM 4 H3 LYS 1 20.370 27.010 15.600 1.00 0.00 +ATOM 5 CA LYS 1 21.340 25.220 15.420 1.00 0.00 +ATOM 6 HA LYS 1 21.780 24.700 14.690 1.00 0.00 +ATOM 7 CB LYS 1 22.320 25.590 16.540 1.00 0.00 +ATOM 8 HB1 LYS 1 23.080 26.100 16.150 1.00 0.00 +ATOM 9 HB2 LYS 1 21.840 26.160 17.210 1.00 0.00 +ATOM 10 CG LYS 1 22.900 24.400 17.290 1.00 0.00 +ATOM 11 HG1 LYS 1 22.210 24.040 17.910 1.00 0.00 +ATOM 12 HG2 LYS 1 23.150 23.690 16.620 1.00 0.00 +ATOM 13 CD LYS 1 24.140 24.800 18.080 1.00 0.00 +ATOM 14 HD1 LYS 1 24.900 24.980 17.450 1.00 0.00 +ATOM 15 HD2 LYS 1 23.940 25.620 18.610 1.00 0.00 +ATOM 16 CE LYS 1 24.510 23.660 19.010 1.00 0.00 +ATOM 17 HE1 LYS 1 23.860 23.610 19.770 1.00 0.00 +ATOM 18 HE2 LYS 1 24.510 22.790 18.520 1.00 0.00 +ATOM 19 NZ LYS 1 25.870 23.920 19.550 1.00 0.00 +ATOM 20 HZ1 LYS 1 26.140 23.180 20.170 1.00 0.00 +ATOM 21 HZ2 LYS 1 26.530 23.970 18.790 1.00 0.00 +ATOM 22 HZ3 LYS 1 25.870 24.790 20.050 1.00 0.00 +ATOM 23 C LYS 1 20.190 24.410 16.010 1.00 0.00 +ATOM 24 O LYS 1 19.400 24.960 16.770 1.00 0.00 +ATOM 25 N VAL 2 20.190 23.110 15.810 1.00 0.00 +ATOM 26 H VAL 2 20.810 22.750 15.110 1.00 0.00 +ATOM 27 CA VAL 2 19.350 22.150 16.520 1.00 0.00 +ATOM 28 HA VAL 2 18.620 22.670 16.950 1.00 0.00 +ATOM 29 CB VAL 2 18.590 21.180 15.620 1.00 0.00 +ATOM 30 HB VAL 2 19.310 20.670 15.150 1.00 0.00 +ATOM 31 CG1 VAL 2 17.700 20.230 16.420 1.00 0.00 +ATOM 32 1HG1 VAL 2 17.220 19.620 15.790 1.00 0.00 +ATOM 33 2HG1 VAL 2 18.270 19.700 17.040 1.00 0.00 +ATOM 34 3HG1 VAL 2 17.030 20.760 16.940 1.00 0.00 +ATOM 35 CG2 VAL 2 17.740 21.860 14.560 1.00 0.00 +ATOM 36 1HG2 VAL 2 17.280 21.170 14.010 1.00 0.00 +ATOM 37 2HG2 VAL 2 17.070 22.450 15.000 1.00 0.00 +ATOM 38 3HG2 VAL 2 18.330 22.420 13.970 1.00 0.00 +ATOM 39 C VAL 2 20.250 21.460 17.560 1.00 0.00 +ATOM 40 O VAL 2 21.210 20.760 17.190 1.00 0.00 +ATOM 41 N PHE 3 19.940 21.700 18.810 1.00 0.00 +ATOM 42 H PHE 3 19.200 22.340 19.010 1.00 0.00 +ATOM 43 CA PHE 3 20.640 21.050 19.930 1.00 0.00 +ATOM 44 HA PHE 3 21.600 21.120 19.680 1.00 0.00 +ATOM 45 CB PHE 3 20.420 21.780 21.260 1.00 0.00 +ATOM 46 HB1 PHE 3 19.500 22.170 21.270 1.00 0.00 +ATOM 47 HB2 PHE 3 20.510 21.130 22.010 1.00 0.00 +ATOM 48 CG PHE 3 21.390 22.890 21.470 1.00 0.00 +ATOM 49 CD1 PHE 3 21.120 24.200 21.050 1.00 0.00 +ATOM 50 HD1 PHE 3 20.260 24.400 20.580 1.00 0.00 +ATOM 51 CD2 PHE 3 22.450 22.710 22.380 1.00 0.00 +ATOM 52 HD2 PHE 3 22.580 21.810 22.800 1.00 0.00 +ATOM 53 CE1 PHE 3 22.030 25.230 21.280 1.00 0.00 +ATOM 54 HE1 PHE 3 21.930 26.100 20.810 1.00 0.00 +ATOM 55 CE2 PHE 3 23.320 23.740 22.690 1.00 0.00 +ATOM 56 HE2 PHE 3 24.110 23.570 23.280 1.00 0.00 +ATOM 57 CZ PHE 3 23.090 25.020 22.180 1.00 0.00 +ATOM 58 HZ PHE 3 23.670 25.790 22.460 1.00 0.00 +ATOM 59 C PHE 3 20.190 19.590 20.080 1.00 0.00 +ATOM 60 O PHE 3 18.970 19.310 19.990 1.00 0.00 +ATOM 61 N GLY 4 21.170 18.790 20.520 1.00 0.00 +ATOM 62 H GLY 4 22.120 19.100 20.530 1.00 0.00 +ATOM 63 CA GLY 4 20.820 17.430 20.980 1.00 0.00 +ATOM 64 HA1 GLY 4 20.070 17.070 20.420 1.00 0.00 +ATOM 65 HA2 GLY 4 21.610 16.830 20.910 1.00 0.00 +ATOM 66 C GLY 4 20.370 17.570 22.430 1.00 0.00 +ATOM 67 O GLY 4 20.750 18.550 23.070 1.00 0.00 +ATOM 68 N ARG 5 19.500 16.690 22.880 1.00 0.00 +ATOM 69 H ARG 5 19.160 15.990 22.250 1.00 0.00 +ATOM 70 CA ARG 5 19.010 16.690 24.260 1.00 0.00 +ATOM 71 HA ARG 5 18.430 17.490 24.330 1.00 0.00 +ATOM 72 CB ARG 5 18.210 15.410 24.520 1.00 0.00 +ATOM 73 HB1 ARG 5 17.450 15.370 23.880 1.00 0.00 +ATOM 74 HB2 ARG 5 18.810 14.620 24.380 1.00 0.00 +ATOM 75 CG ARG 5 17.660 15.350 25.930 1.00 0.00 +ATOM 76 HG1 ARG 5 18.420 15.320 26.580 1.00 0.00 +ATOM 77 HG2 ARG 5 17.100 16.160 26.100 1.00 0.00 +ATOM 78 CD ARG 5 16.830 14.150 26.130 1.00 0.00 +ATOM 79 HD1 ARG 5 16.490 14.140 27.070 1.00 0.00 +ATOM 80 HD2 ARG 5 16.050 14.200 25.500 1.00 0.00 +ATOM 81 NE ARG 5 17.510 12.900 25.890 1.00 0.00 +ATOM 82 HE ARG 5 17.470 12.550 24.960 1.00 0.00 +ATOM 83 CZ ARG 5 18.180 12.160 26.750 1.00 0.00 +ATOM 84 NH1 ARG 5 18.290 12.480 28.040 1.00 0.00 +ATOM 85 1HH1 ARG 5 17.840 13.310 28.380 1.00 0.00 +ATOM 86 2HH1 ARG 5 18.810 11.900 28.660 1.00 0.00 +ATOM 87 NH2 ARG 5 18.700 10.990 26.320 1.00 0.00 +ATOM 88 1HH2 ARG 5 18.560 10.700 25.380 1.00 0.00 +ATOM 89 2HH2 ARG 5 19.210 10.410 26.950 1.00 0.00 +ATOM 90 C ARG 5 20.120 16.880 25.290 1.00 0.00 +ATOM 91 O1 ARG 5 20.120 17.800 26.150 1.00 0.00 +ATOM 92 O2 ARG 5 19.750 16.890 26.600 1.00 0.00 +TER +ENDMDL |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/npt.cpt |
| b |
| Binary file test-data/npt.cpt has changed |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/npt.edr |
| b |
| Binary file test-data/npt.edr has changed |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/npt.gro --- a/test-data/npt.gro Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,38379 +0,0 @@\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 4b4232c98b6e -r a97dcfc23b4b test-data/npt.mdp --- a/test-data/npt.mdp Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,46 +0,0 @@ -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 4b4232c98b6e -r a97dcfc23b4b test-data/npt.pdb --- a/test-data/npt.pdb Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,38382 +0,0 @@\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 4b4232c98b6e -r a97dcfc23b4b test-data/nvt.gro --- a/test-data/nvt.gro Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,38379 +0,0 @@\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' |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/nvt.mdp --- a/test-data/nvt.mdp Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,43 +0,0 @@ -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 |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/nvt.pdb --- a/test-data/nvt.pdb Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,38382 +0,0 @@\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' |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/nvt.tpr |
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| Binary file test-data/nvt.tpr has changed |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/nvt.trr |
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| Binary file test-data/nvt.trr has changed |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/nvt.xtc |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/outp.edr |
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| Binary file test-data/outp.edr has changed |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/outp.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outp.tabular Wed May 20 13:00:42 2020 -0400 |
| b |
| @@ -0,0 +1,11 @@ +0.000000 -875.856201 -565.607910 -561.483948 +0.100000 -937.817383 -652.096558 -563.097961 +0.200000 -1076.080811 -764.079712 -564.585632 +0.300000 -1128.099854 -869.548645 -563.387207 +0.400000 -1194.588623 -941.101868 -563.371216 +0.500000 -1229.046509 -942.665039 -564.364685 +0.600000 -1304.865845 -1042.604736 -565.530396 +0.700000 -1355.996216 -1110.028687 -566.059509 +0.800000 -1339.003906 -1115.218750 -566.635681 +0.900000 -1310.706909 -1073.441406 -566.569702 +1.000000 -1306.671997 -1089.731323 -566.253174 |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/outp.xvg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outp.xvg Wed May 20 13:00:42 2020 -0400 |
| b |
| @@ -0,0 +1,37 @@ +# This file was created Tue May 19 15:42:53 2020 +# Created by: +# :-) GROMACS - gmx energy, 2019.1 (-: +# +# Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx +# Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1 +# Working dir: /tmp/tmprwcs9m2t/job_working_directory/000/17/working +# Command line: +# gmx energy -f ./edr_input.edr -o ./energy.xvg +# gmx energy is part of G R O M A C S: +# +# GROningen Mixture of Alchemy and Childrens' Stories +# +@ title "GROMACS Energies" +@ xaxis label "Time (ps)" +@ yaxis label "(kJ/mol)" +@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 "Conserved En." + 0.000000 -875.856201 -565.607910 -561.483948 + 0.100000 -937.817383 -652.096558 -563.097961 + 0.200000 -1076.080811 -764.079712 -564.585632 + 0.300000 -1128.099854 -869.548645 -563.387207 + 0.400000 -1194.588623 -941.101868 -563.371216 + 0.500000 -1229.046509 -942.665039 -564.364685 + 0.600000 -1304.865845 -1042.604736 -565.530396 + 0.700000 -1355.996216 -1110.028687 -566.059509 + 0.800000 -1339.003906 -1115.218750 -566.635681 + 0.900000 -1310.706909 -1073.441406 -566.569702 + 1.000000 -1306.671997 -1089.731323 -566.253174 |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/posre_cl.itp --- a/test-data/posre_cl.itp Fri May 08 07:41:18 2020 -0400 +++ b/test-data/posre_cl.itp Wed May 20 13:00:42 2020 -0400 |
| [ |
| @@ -1,12 +1,5 @@ -; 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 + 93 1 500 600 700 + 94 1 500 600 700 |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/posres.itp --- a/test-data/posres.itp Fri May 08 07:41:18 2020 -0400 +++ b/test-data/posres.itp Wed May 20 13:00:42 2020 -0400 |
| b |
| b'@@ -48,961 +48,3 @@\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 1000 1000\n- 244 1 1000 1000 1000\n- 245 1 1000 1000 1000\n- 246 1 1000 1000 1000\n- 248 1 1000 1000 1000\n- 251 1 1000 1000 1000\n- 252 1 1000 1000 1000\n- 253 1 1000 1000 1000\n- 255 1 1000 1000 1000\n- 257 1 1000 1000 1000\n- 260 1 1000 1000 1000\n- 262 1 1000 1000 1000\n- 266 1 1000 1000 1000\n- 270 1 1000 1000 1000\n- 271 1 1000 1000 1000\n- 272 1 1000 1000 1000\n- 274 1 1000 1000 1000\n- 276 1 1000 1000 1000\n- 279 1 1000 1000 1000\n- 280 1 1000 1000 1000\n- 281 1 1000 1000 1000\n- 282 1 1000 1000 1000\n- 283 1 1000 1000 1000\n- 284 1 1000 1000 1000\n- 286 1 1000 1000 1000\n- 288 1 1000 1000 1000\n- 291 1 1000 1000 1000\n- 292 1 1000 1000 1000\n- 293 1 1000 1000 1000\n- 296 1 1000 1000 1000\n- 297 1 1000 1000 1000\n- 298 1 1000 1000 1000\n- 300 1 1000 1000 1000\n- 302 1 1000 1000 1000\n- 305 1 1000 1000 1000\n- 306 1 1000 1000 1000\n- 308 1 1000 1000 1000\n- 310 1 1000 1000 1000\n- 312 1 1000 1000 1000\n- 314 1 1000 1000 1000\n- 315 1 1000 1000 1000\n- 317 1 1000 1000 1000\n- 318 1 1000 1000 1000\n- 319 1 1000 1000 1000\n- 321 1 1000 1000 1000\n- 323 1 1000 1000 1000\n- 326 1 1000 1000 1000\n- 329 1 1000 1000 1000\n- 332 1 1000 1000 1000\n- 334 '..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 4b4232c98b6e -r a97dcfc23b4b test-data/processed.gro --- a/test-data/processed.gro Fri May 08 07:41:18 2020 -0400 +++ b/test-data/processed.gro Wed May 20 13:00:42 2020 -0400 |
| b |
| b'@@ -1,5 +1,5 @@\n-LYSOZYME\n- 2194\n+TEST\n+ 92\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@@ -90,2108 +90,6 @@\n 5ARG HH21 88 3.311 0.655 -0.147\n 5ARG HH22 89 3.376 0.626 0.010\n 5ARG C 90 3.467 1.273 -0.156\n- 5ARG O 91 3.467 1.365 -0.070\n- 6CYS N 92 3.567 1.185 -0.161\n- 6CYS H 93 3.567 1.116 -0.233\n- 6CYS CA 94 3.678 1.187 -0.065\n- 6CYS HA 95 3.631 1.202 0.022\n- 6CYS CB 96 3.749 1.053 -0.062\n- 6CYS HB1 97 3.770 1.034 -0.158\n- 6CYS HB2 98 3.834 1.072 -0.013\n- 6CYS SG 99 3.654 0.920 0.014\n- 6CYS C 100 3.775 1.305 -0.078\n- 6CYS O 101 3.815 1.361 0.026\n- 7GLU N 102 3.786 1.348 -0.202\n- 7GLU H 103 3.740 1.300 -0.276\n- 7GLU CA 104 3.868 1.469 -0.231\n- 7GLU HA 105 3.960 1.455 -0.193\n- 7GLU CB 106 3.878 1.485 -0.382\n- 7GLU HB1 107 3.923 1.402 -0.417\n- 7GLU HB2 108 3.785 1.489 -0.417\n- 7GLU CG 109 3.954 1.605 -0.438\n- 7GLU HG1 110 3.913 1.687 -0.399\n- 7GLU HG2 111 4.049 1.598 -0.407\n- 7GLU CD 112 3.958 1.624 -0.587\n- 7GLU OE1 113 3.867 1.564 -0.649\n- 7GLU OE2 114 4.042 1.695 -0.638\n- 7GLU C 115 3.805 1.593 -0.166\n- 7GLU O 116 3.874 1.673 -0.101\n- 8LEU N 117 3.674 1.605 -0.182\n- 8LEU H 118 3.626 1.535 -0.235\n- 8LEU CA 119 3.596 1.716 -0.125\n- 8LEU HA 120 3.640 1.801 -0.156\n- 8LEU CB 121 3.453 1.717 -0.181\n- 8LEU HB1 122 3.457 1.722 -0.281\n- 8LEU HB2 123 3.406 1.633 -0.153\n- 8LEU CG 124 3.372 1.835 -0.131\n- 8LEU HG 125 3.378 1.842 -0.031\n- 8LEU CD1 126 3.430 1.966 -0.184\n- 8LEU HD11 127 3.376 2.043 -0.150\n- 8LEU HD12 128 3.524 1.975 -0.153\n- 8LEU HD13 129 3.427 1.965 -0.284\n- 8LEU CD2 130 3.225 1.814 -0.160\n- 8LEU HD21 131 3.172 1.893 -0.126\n- 8LEU HD22 132 3.211 1.805 -0.258\n- 8LEU HD23 133 3.193 1.731 -0.114\n- 8LEU C 134 3.605 1.713 0.027\n- 8LEU O 135 3.616 1.817 0.092\n- 9ALA N 136 3.575 1.598 0.083\n- 9ALA H 137 3.546 1.522 0.024\n- 9ALA CA 138 3.584 1.576 0.228\n- 9ALA HA 139 3.508 1.626 0.269\n- 9ALA CB 140 3.566 1.429 0.262\n- 9ALA HB1 141 3.572 1.416 0.361\n- 9ALA HB2 142 3.476 1.398 0.230\n- 9ALA HB3 143 3.637 1.375 0.218\n- 9ALA C 144 3.714 1.631 0.284\n- 9ALA O 145 3.715 1.698 0.390\n- 10ALA N 146 3.827 1.598 0.220\n- 10ALA H 147 3.820 1.539 0.140\n- 10ALA CA 148 3.961 1.643 0.262\n- 10ALA HA 149 3.969 1.619 0.358\n- 10ALA CB 150 4.071 1.571 0.184\n- 10ALA HB1 151 4.160 1.603 0.215\n- 10ALA HB2 152 4.064 1.472 0.201\n- 10ALA HB3 153 4.060 1.589 0.086\n- 10ALA C 154 3.974 1.794 0.246\n- 10ALA O 155 4.019 1.850 0.347\n- 11ALA N 156 3.923 1.852 0.139\n- 11ALA H 157 3.881 1.795 0.067\n- 11ALA CA 158 3.926 1.998 0.122\n- 11ALA HA 159 4.023 2.023 0.133\n- 11ALA CB 160 3.887 2.042 -0.018\n- 11ALA HB1 161 3.891 2.142 -0.024\n- 11ALA HB2 162 3.950 2.002 -0.084\n- 11ALA HB3 163 3.794 2.011 -0.037\n- 11ALA C 164 3.849 2.070 0.232\n- 11ALA O 165 3.895 2.166 0.295\n- 12MET N 166 3.729 2.021 0.259\n- 12MET H 167 3.697 1.942 0.207\n- 12MET CA 168 3.640 2.078 0.361\n- 12MET HA 169 3.634 2.175 0.339\n- 12MET CB 170 '..b'63 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+ 5ARG O1 91 3.467 1.365 -0.070\n+ 5ARG O2 92 3.430 1.274 -0.025\n 5.90620 6.84510 3.05170\n' |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/solv.gro --- a/test-data/solv.gro Fri May 08 07:41:18 2020 -0400 +++ b/test-data/solv.gro Wed May 20 13:00:42 2020 -0400 |
| b |
| b'@@ -1,38395 +1,6733 @@\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- '..b'51 3.745\n+ 2190SOL OW 6645 3.955 3.575 4.207\n+ 2190SOL HW1 6646 3.989 3.652 4.261\n+ 2190SOL HW2 6647 3.999 3.575 4.117\n+ 2191SOL OW 6648 3.751 3.458 3.841\n+ 2191SOL HW1 6649 3.732 3.362 3.862\n+ 2191SOL HW2 6650 3.718 3.516 3.916\n+ 2192SOL OW 6651 4.021 1.897 3.895\n+ 2192SOL HW1 6652 4.070 1.981 3.874\n+ 2192SOL HW2 6653 4.083 1.832 3.940\n+ 2193SOL OW 6654 3.732 3.188 3.924\n+ 2193SOL HW1 6655 3.639 3.209 3.893\n+ 2193SOL HW2 6656 3.742 3.089 3.937\n+ 2194SOL OW 6657 3.799 2.207 3.757\n+ 2194SOL HW1 6658 3.707 2.179 3.728\n+ 2194SOL HW2 6659 3.830 2.284 3.701\n+ 2195SOL OW 6660 3.796 2.028 4.042\n+ 2195SOL HW1 6661 3.779 2.111 3.988\n+ 2195SOL HW2 6662 3.886 1.991 4.020\n+ 2196SOL OW 6663 3.763 2.939 4.024\n+ 2196SOL HW1 6664 3.862 2.928 4.015\n+ 2196SOL HW2 6665 3.723 2.853 4.056\n+ 2197SOL OW 6666 3.954 4.352 0.113\n+ 2197SOL HW1 6667 3.861 4.350 0.150\n+ 2197SOL HW2 6668 3.955 4.313 0.021\n+ 2198SOL OW 6669 3.949 3.999 0.996\n+ 2198SOL HW1 6670 3.984 3.982 1.088\n+ 2198SOL HW2 6671 3.861 3.954 0.984\n+ 2199SOL OW 6672 3.743 4.092 0.647\n+ 2199SOL HW1 6673 3.661 4.135 0.686\n+ 2199SOL HW2 6674 3.715 4.019 0.584\n+ 2200SOL OW 6675 3.926 4.009 1.498\n+ 2200SOL HW1 6676 3.846 4.069 1.485\n+ 2200SOL HW2 6677 3.916 3.960 1.584\n+ 2201SOL OW 6678 4.031 3.937 1.231\n+ 2201SOL HW1 6679 4.008 3.974 1.321\n+ 2201SOL HW2 6680 4.001 3.842 1.225\n+ 2202SOL OW 6681 4.031 3.787 0.618\n+ 2202SOL HW1 6682 4.020 3.881 0.651\n+ 2202SOL HW2 6683 4.026 3.724 0.695\n+ 2203SOL OW 6684 3.796 3.890 0.318\n+ 2203SOL HW1 6685 3.779 3.973 0.264\n+ 2203SOL HW2 6686 3.886 3.853 0.296\n+ 2204SOL OW 6687 3.954 4.352 1.975\n+ 2204SOL HW1 6688 3.861 4.350 2.012\n+ 2204SOL HW2 6689 3.955 4.313 1.883\n+ 2205SOL OW 6690 3.949 3.999 2.858\n+ 2205SOL HW1 6691 3.984 3.982 2.950\n+ 2205SOL HW2 6692 3.861 3.954 2.846\n+ 2206SOL OW 6693 3.743 4.092 2.509\n+ 2206SOL HW1 6694 3.661 4.135 2.548\n+ 2206SOL HW2 6695 3.715 4.019 2.446\n+ 2207SOL OW 6696 3.926 4.009 3.360\n+ 2207SOL HW1 6697 3.846 4.069 3.347\n+ 2207SOL HW2 6698 3.916 3.960 3.446\n+ 2208SOL OW 6699 4.021 3.759 2.033\n+ 2208SOL HW1 6700 4.070 3.843 2.012\n+ 2208SOL HW2 6701 4.083 3.694 2.078\n+ 2209SOL OW 6702 4.031 3.937 3.093\n+ 2209SOL HW1 6703 4.008 3.974 3.183\n+ 2209SOL HW2 6704 4.001 3.842 3.087\n+ 2210SOL OW 6705 4.031 3.787 2.480\n+ 2210SOL HW1 6706 4.020 3.881 2.513\n+ 2210SOL HW2 6707 4.026 3.724 2.557\n+ 2211SOL OW 6708 3.799 4.069 1.895\n+ 2211SOL HW1 6709 3.707 4.041 1.866\n+ 2211SOL HW2 6710 3.830 4.146 1.839\n+ 2212SOL OW 6711 3.796 3.890 2.180\n+ 2212SOL HW1 6712 3.779 3.973 2.126\n+ 2212SOL HW2 6713 3.886 3.853 2.158\n+ 2213SOL OW 6714 3.954 4.352 3.837\n+ 2213SOL HW1 6715 3.861 4.350 3.874\n+ 2213SOL HW2 6716 3.955 4.313 3.745\n+ 2214SOL OW 6717 4.021 3.759 3.895\n+ 2214SOL HW1 6718 4.070 3.843 3.874\n+ 2214SOL HW2 6719 4.083 3.694 3.940\n+ 2215SOL OW 6720 3.799 4.069 3.757\n+ 2215SOL HW1 6721 3.707 4.041 3.728\n+ 2215SOL HW2 6722 3.830 4.146 3.701\n+ 2216SOL OW 6723 3.796 3.890 4.042\n+ 2216SOL HW1 6724 3.779 3.973 3.988\n+ 2216SOL HW2 6725 3.886 3.853 4.020\n+ 2217SOL OW 6726 4.152 4.148 4.244\n+ 2217SOL HW1 6727 4.182 4.076 4.182\n+ 2217SOL HW2 6728 4.113 4.108 4.327\n+ 2218CL CL 6729 0.865 2.210 2.057\n+ 2219CL CL 6730 2.879 3.763 2.615\n+ 4.09123 4.09123 4.09123\n' |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/solv_ions.gro --- a/test-data/solv_ions.gro Fri May 08 07:41:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,38379 +0,0 @@\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 4b4232c98b6e -r a97dcfc23b4b test-data/str_ions.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/str_ions.gro Wed May 20 13:00:42 2020 -0400 |
| b |
| @@ -0,0 +1,97 @@ +TEST in water + 94 + 1LYS N 1 2.081 2.649 1.487 + 1LYS H1 2 2.157 2.703 1.449 + 1LYS H2 3 2.015 2.629 1.415 + 1LYS H3 4 2.037 2.701 1.560 + 1LYS CA 5 2.134 2.522 1.542 + 1LYS HA 6 2.178 2.470 1.469 + 1LYS CB 7 2.232 2.559 1.654 + 1LYS HB1 8 2.308 2.610 1.615 + 1LYS HB2 9 2.184 2.616 1.721 + 1LYS CG 10 2.290 2.440 1.729 + 1LYS HG1 11 2.221 2.404 1.791 + 1LYS HG2 12 2.315 2.369 1.662 + 1LYS CD 13 2.414 2.480 1.808 + 1LYS HD1 14 2.490 2.498 1.745 + 1LYS HD2 15 2.394 2.562 1.861 + 1LYS CE 16 2.451 2.366 1.901 + 1LYS HE1 17 2.386 2.361 1.977 + 1LYS HE2 18 2.451 2.279 1.852 + 1LYS NZ 19 2.587 2.392 1.955 + 1LYS HZ1 20 2.614 2.318 2.017 + 1LYS HZ2 21 2.653 2.397 1.879 + 1LYS HZ3 22 2.587 2.479 2.005 + 1LYS C 23 2.019 2.441 1.601 + 1LYS O 24 1.940 2.496 1.677 + 2VAL N 25 2.019 2.311 1.581 + 2VAL H 26 2.081 2.275 1.511 + 2VAL CA 27 1.935 2.215 1.652 + 2VAL HA 28 1.862 2.267 1.695 + 2VAL CB 29 1.859 2.118 1.562 + 2VAL HB 30 1.931 2.067 1.515 + 2VAL CG1 31 1.770 2.023 1.642 + 2VAL HG11 32 1.722 1.962 1.579 + 2VAL HG12 33 1.827 1.970 1.704 + 2VAL HG13 34 1.703 2.076 1.694 + 2VAL CG2 35 1.774 2.186 1.456 + 2VAL HG21 36 1.728 2.117 1.401 + 2VAL HG22 37 1.707 2.245 1.500 + 2VAL HG23 38 1.833 2.242 1.397 + 2VAL C 39 2.025 2.146 1.756 + 2VAL O 40 2.121 2.076 1.719 + 3PHE N 41 1.994 2.170 1.881 + 3PHE H 42 1.920 2.234 1.901 + 3PHE CA 43 2.064 2.105 1.993 + 3PHE HA 44 2.160 2.112 1.968 + 3PHE CB 45 2.042 2.178 2.126 + 3PHE HB1 46 1.950 2.217 2.127 + 3PHE HB2 47 2.051 2.113 2.201 + 3PHE CG 48 2.139 2.289 2.147 + 3PHE CD1 49 2.112 2.420 2.105 + 3PHE HD1 50 2.026 2.440 2.058 + 3PHE CD2 51 2.245 2.271 2.238 + 3PHE HD2 52 2.258 2.181 2.280 + 3PHE CE1 53 2.203 2.523 2.128 + 3PHE HE1 54 2.193 2.610 2.081 + 3PHE CE2 55 2.332 2.374 2.269 + 3PHE HE2 56 2.411 2.357 2.328 + 3PHE CZ 57 2.309 2.502 2.218 + 3PHE HZ 58 2.367 2.579 2.246 + 3PHE C 59 2.019 1.959 2.008 + 3PHE O 60 1.897 1.931 1.999 + 4GLY N 61 2.117 1.879 2.052 + 4GLY H 62 2.212 1.910 2.053 + 4GLY CA 63 2.082 1.743 2.098 + 4GLY HA1 64 2.007 1.707 2.042 + 4GLY HA2 65 2.161 1.683 2.091 + 4GLY C 66 2.037 1.757 2.243 + 4GLY O 67 2.075 1.855 2.307 + 5ARG N 68 1.950 1.669 2.288 + 5ARG H 69 1.916 1.599 2.225 + 5ARG CA 70 1.901 1.669 2.426 + 5ARG HA 71 1.843 1.749 2.433 + 5ARG CB 72 1.821 1.541 2.452 + 5ARG HB1 73 1.745 1.537 2.388 + 5ARG HB2 74 1.881 1.462 2.438 + 5ARG CG 75 1.766 1.535 2.593 + 5ARG HG1 76 1.842 1.532 2.658 + 5ARG HG2 77 1.710 1.616 2.610 + 5ARG CD 78 1.683 1.415 2.613 + 5ARG HD1 79 1.649 1.414 2.707 + 5ARG HD2 80 1.605 1.420 2.550 + 5ARG NE 81 1.751 1.290 2.589 + 5ARG HE 82 1.747 1.255 2.496 + 5ARG CZ 83 1.818 1.216 2.675 + 5ARG NH1 84 1.829 1.248 2.804 + 5ARG HH11 85 1.784 1.331 2.838 + 5ARG HH12 86 1.881 1.190 2.866 + 5ARG NH2 87 1.870 1.099 2.632 + 5ARG HH21 88 1.856 1.070 2.538 + 5ARG HH22 89 1.921 1.041 2.695 + 5ARG C 90 2.012 1.688 2.529 + 5ARG O1 91 2.012 1.780 2.615 + 5ARG O2 92 1.975 1.689 2.660 + 6CL CL 6729 0.865 2.210 2.057 + 6CL CL 6730 2.879 3.763 2.615 + 4.09123 4.09123 4.09123 |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/topol.top --- a/test-data/topol.top Fri May 08 07:41:18 2020 -0400 +++ b/test-data/topol.top Wed May 20 13:00:42 2020 -0400 |
| [ |
| b"@@ -2,18 +2,18 @@\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+;\tAt date: Tue May 12 12:59:21 2020\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+;\tExecutable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/__gromacs@2019.1\n+;\tWorking dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working\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+;\t gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all\n ;\tForce field was read from the standard GROMACS share directory.\n ;\n \n@@ -22,7 +22,7 @@\n \n [ moleculetype ]\n ; Name nrexcl\n-Protein_chain_A 3\n+Protein 3\n \n [ atoms ]\n ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n@@ -97,10 +97,10 @@\n 65 opls_140 4 GLY HA2 21 0.06 1.008\n 66 opls_235 4 GLY C 22 0.5 12.011\n 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2\n-; residue 5 ARG rtp ARG q +1.0\n+; residue 5 ARG rtp ARG q 0.0\n 68 opls_238 5 ARG N 23 -0.5 14.0067\n 69 opls_241 5 ARG H 23 0.3 1.008\n- 70 opls_224B 5 ARG CA 23 0.14 12.011\n+ 70 opls_283 5 ARG CA 23 0.04 12.011\n 71 opls_140 5 ARG HA 23 0.06 1.008\n 72 opls_136 5 ARG CB 24 -0.12 12.011\n 73 opls_140 5 ARG HB1 24 0.06 1.008\n@@ -120,2001 +120,9 @@\n 87 opls_300 5 ARG NH2 29 -0.8 14.0067\n 88 opls_301 5 ARG HH21 29 0.46 1.008\n 89 opls_301 5 ARG HH22 29 0.46 1.008\n- 90 opls_235 5 ARG C 30 0.5 12.011\n- 91 opls_236 5 ARG O 30 -0.5 15.9994 ; qtot 3\n-; residue 6 CYS rtp CYS2 q 0.0\n- 92 opls_238 6 CYS N 31 -0.5 14.0067\n- 93 opls_241 6 CYS H 31 0.3 1.008\n- 94 opls_224B 6 CYS CA 31 0.14 12.011\n- 95 opls_140 6 CYS HA 31 0.06 1.008\n- 96 opls_214 6 CYS CB 32 0.0975 12.011\n- 97 opls_140 6 CYS HB1 32 0.06 1.008\n- 98 opls_140 6 CYS HB2 32 0.06 1.008\n- 99 opls_203 6 CYS SG 32 -0.2175 32.06\n- 100 opls_235 6 CYS C 33 0.5 12.011\n- 101 opls_236 6 CYS O 33 -0.5 15.9994 ; qtot 3\n-; residue 7 GLU rtp GLU q -1.0\n- 102 opls_238 7 GLU N 34 -0.5 14.0067\n- 103 opls_241 7 GLU H 34 0.3 1.008\n- 104 opls_224B 7 GLU CA 34 0.14 12.011\n- 105 opls_140 7 GLU HA 34 0.06 1.008\n- 106 opls_136 7 GLU CB 35 -0.12 12.011\n- 107 opls_140 7 GLU HB1 35 0.06 1.008\n- 108 opls_140 7 GLU HB2 35 0.06 1.008\n- 109 opls_274 7 GLU CG 36 -0.22 12.011\n- 110 opls_140 7 GLU HG1 36 0.06 1.008\n- 111 opls_140 7 GLU HG2 36 0.06 1.008\n- 112 opls_271 7 GLU CD 37 0.7 12.011\n- 113 opls_272 7 GLU OE1 37 -0.8 15.9994\n"..b'39 1637 1638 1 improper_O_C_X_Y\n- 1637 1641 1639 1640 1 improper_Z_N_X_Y\n- 1641 1663 1661 1662 1 improper_O_C_X_Y\n- 1643 1646 1649 1647 1 improper_Z_CA_X_Y\n- 1646 1650 1647 1648 1 improper_Z_CA_X_Y\n- 1647 1652 1650 1651 1 improper_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@@ -18401,9 +902,8 @@\n \n [ system ]\n ; Name\n-LYSOZYME\n+TEST\n \n [ molecules ]\n ; Compound #mols\n-Protein_chain_A 1\n-SOL 78\n+Protein 1\n' |
| b |
| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/topol_solv.top --- a/test-data/topol_solv.top Fri May 08 07:41:18 2020 -0400 +++ b/test-data/topol_solv.top Wed May 20 13:00:42 2020 -0400 |
| [ |
| b"@@ -2,18 +2,18 @@\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+;\tAt date: Tue May 12 12:59:21 2020\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+;\tExecutable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/__gromacs@2019.1\n+;\tWorking dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working\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+;\t gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all\n ;\tForce field was read from the standard GROMACS share directory.\n ;\n \n@@ -22,7 +22,7 @@\n \n [ moleculetype ]\n ; Name nrexcl\n-Protein_chain_A 3\n+Protein 3\n \n [ atoms ]\n ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n@@ -97,10 +97,10 @@\n 65 opls_140 4 GLY HA2 21 0.06 1.008\n 66 opls_235 4 GLY C 22 0.5 12.011\n 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2\n-; residue 5 ARG rtp ARG q +1.0\n+; residue 5 ARG rtp ARG q 0.0\n 68 opls_238 5 ARG N 23 -0.5 14.0067\n 69 opls_241 5 ARG H 23 0.3 1.008\n- 70 opls_224B 5 ARG CA 23 0.14 12.011\n+ 70 opls_283 5 ARG CA 23 0.04 12.011\n 71 opls_140 5 ARG HA 23 0.06 1.008\n 72 opls_136 5 ARG CB 24 -0.12 12.011\n 73 opls_140 5 ARG HB1 24 0.06 1.008\n@@ -120,2001 +120,9 @@\n 87 opls_300 5 ARG NH2 29 -0.8 14.0067\n 88 opls_301 5 ARG HH21 29 0.46 1.008\n 89 opls_301 5 ARG HH22 29 0.46 1.008\n- 90 opls_235 5 ARG C 30 0.5 12.011\n- 91 opls_236 5 ARG O 30 -0.5 15.9994 ; qtot 3\n-; residue 6 CYS rtp CYS2 q 0.0\n- 92 opls_238 6 CYS N 31 -0.5 14.0067\n- 93 opls_241 6 CYS H 31 0.3 1.008\n- 94 opls_224B 6 CYS CA 31 0.14 12.011\n- 95 opls_140 6 CYS HA 31 0.06 1.008\n- 96 opls_214 6 CYS CB 32 0.0975 12.011\n- 97 opls_140 6 CYS HB1 32 0.06 1.008\n- 98 opls_140 6 CYS HB2 32 0.06 1.008\n- 99 opls_203 6 CYS SG 32 -0.2175 32.06\n- 100 opls_235 6 CYS C 33 0.5 12.011\n- 101 opls_236 6 CYS O 33 -0.5 15.9994 ; qtot 3\n-; residue 7 GLU rtp GLU q -1.0\n- 102 opls_238 7 GLU N 34 -0.5 14.0067\n- 103 opls_241 7 GLU H 34 0.3 1.008\n- 104 opls_224B 7 GLU CA 34 0.14 12.011\n- 105 opls_140 7 GLU HA 34 0.06 1.008\n- 106 opls_136 7 GLU CB 35 -0.12 12.011\n- 107 opls_140 7 GLU HB1 35 0.06 1.008\n- 108 opls_140 7 GLU HB2 35 0.06 1.008\n- 109 opls_274 7 GLU CG 36 -0.22 12.011\n- 110 opls_140 7 GLU HG1 36 0.06 1.008\n- 111 opls_140 7 GLU HG2 36 0.06 1.008\n- 112 opls_271 7 GLU CD 37 0.7 12.011\n- 113 opls_272 7 GLU OE1 37 -0.8 15.9994\n"..b'roper_Z_N_X_Y\n- 1641 1663 1661 1662 1 improper_O_C_X_Y\n- 1643 1646 1649 1647 1 improper_Z_CA_X_Y\n- 1646 1650 1647 1648 1 improper_Z_CA_X_Y\n- 1647 1652 1650 1651 1 improper_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@@ -18401,11 +902,9 @@\n \n [ system ]\n ; Name\n-LYSOZYME in water\n+TEST in water\n \n [ molecules ]\n ; Compound #mols\n-Protein_chain_A 1\n-SOL 78\n-SOL 12058\n-CL 8\n+Protein 1\n+CL 2\n' |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/trjcat.xtc |
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| diff -r 4b4232c98b6e -r a97dcfc23b4b test-data/trjconv.xtc |
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| Binary file test-data/trjconv.xtc has changed |