# HG changeset patch # User chemteam # Date 1657629862 0 # Node ID 17c12d5cb336616e879bc10c0fb9fa8f0d5dad24 # Parent 04abdf96978b0f846cce417f054b177b8b453679 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d diff -r 04abdf96978b -r 17c12d5cb336 test-data/check_compare_energy.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_compare_energy.txt Tue Jul 12 12:44:22 2022 +0000 @@ -0,0 +1,199 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -e ./ener1.edr -e2 ./ener2.edr -tol 0.1 -abstol 0.1 -lastener Pressure + +Opened ./ener1.edr as single precision energy file +Opened ./ener2.edr as single precision energy file + +Reading energy frame 0 time 0.000 +Reading energy frame 0 time 0.000 +Reading energy frame 1 time 1.000 +Reading energy frame 1 time 0.100 +Reading energy frame 2 time 2.000 +Reading energy frame 2 time 0.200 +Reading energy frame 3 time 3.000 +Reading energy frame 3 time 0.300 +Reading energy frame 4 time 4.000 +Reading energy frame 4 time 0.400 comparing energy file ./ener1.edr and ./ener2.edr + +There are 31 and 50 terms in the energy files + +enm[0] (Bond - -) +enm[30] (T-rest - -) +enm[6] (- - Disper. corr.) +enm[10] (- - Kinetic En.) +enm[11] (- - Total Energy) +enm[12] (- - Conserved En.) +enm[13] (- - Temperature) +enm[14] (- - Pres. DC) +enm[16] (- - Constr. rmsd) +enm[17] (- - Box-X) +enm[18] (- - Box-Y) +enm[19] (- - Box-Z) +enm[20] (- - Volume) +enm[21] (- - Density) +enm[22] (- - pV) +enm[23] (- - Enthalpy) +enm[43] (- - Box-Vel-XX) +enm[44] (- - Box-Vel-YY) +enm[45] (- - Box-Vel-ZZ) +enm[46] (- - T-Protein) +enm[47] (- - T-non-Protein) +enm[48] (- - Lamb-Protein) +enm[49] (- - Lamb-non-Protein) +There are 11 terms to compare in the energy files + +Angle step 0: 659.741, step 0: 174.95 +Proper Dih. step 0: 93.8665, step 0: 8.40722 +Ryckaert-Bell. step 0: 69.404, step 0: 91.4765 +Coulomb-14 step 0: 52.8221, step 0: 135.375 +LJ (SR) step 0: -13.3421, step 0: -8.41078 +Coulomb (SR) step 0: -1790.86, step 0: -2038.4 +Coul. recip. step 0: 959.265, step 0: 615.944 +Potential step 0: 618.021, step 0: -875.856 +Pressure step 0: 901.187, step 0: 149.004 +Vir-XX step 0: -2075.14, step 0: -98.9118 +t (1.000000e+00 - 1.000000e-01) +step (1 - 50) +Angle step 1: 536.268, step 1: 188.647 +Proper Dih. step 1: 88.2, step 1: 17.982 +Ryckaert-Bell. step 1: 67.8373, step 1: 95.8567 +Coulomb-14 step 1: 49.6531, step 1: 108.883 +LJ (SR) step 1: -11.6246, step 1: 9.77759 +Coulomb (SR) step 1: -1784.23, step 1: -2034.55 +Coul. recip. step 1: 951.94, step 1: 546.933 +Potential step 1: 230.009, step 1: -937.817 +Pressure step 1: 893.094, step 1: 60.2446 +Vir-XX step 1: -1778.72, step 1: 128.956 +t (2.000000e+00 - 2.000000e-01) +step (2 - 100) +Angle step 2: 424.105, step 2: 176.128 +Proper Dih. step 2: 81.0497, step 2: 13.4277 +Ryckaert-Bell. step 2: 66.1758, step 2: 112.768 +Coulomb-14 step 2: 47.7305, step 2: 126.537 +LJ (SR) step 2: -0.367874, step 2: -9.48936 +Coulomb (SR) step 2: -1780.95, step 2: -2085.56 +Coul. recip. step 2: 946.125, step 2: 455.54 +Potential step 2: -14.5562, step 2: -1076.08 +Pressure step 2: 675.983, step 2: -57.99 +Vir-XX step 2: -1371.69, step 2: 247.454 +t (3.000000e+00 - 3.000000e-01) +step (3 - 150) +Angle step 3: 237.376, step 3: 205.981 +Proper Dih. step 3: 68.1909, step 3: 18.2245 +Ryckaert-Bell. step 3: 59.979, step 3: 147.317 +Coulomb-14 step 3: 46.4965, step 3: 109.053 +LJ (SR) step 3: -1.62034, step 3: 38.8948 +Coulomb (SR) step 3: -1772, step 3: -2168.63 +Coul. recip. step 3: 935.019, step 3: 399.011 +Potential step 3: -223.77, step 3: -1128.1 +Pressure step 3: 525.266, step 3: 37.3865 +Vir-XX step 3: -964.61, step 3: 59.3395 +t (4.000000e+00 - 4.000000e-01) +step (4 - 200) +Proper Dih. step 4: 59.4324, step 4: 17.8104 +Ryckaert-Bell. step 4: 58.0578, step 4: 110.021 +Coulomb-14 step 4: 48.4256, step 4: 105.922 +LJ (SR) step 4: -5.24827, step 4: 17.1558 +Coulomb (SR) step 4: -1769.41, step 4: -2150.06 +Coul. recip. step 4: 932.888, step 4: 375.412 +Potential step 4: -294.892, step 4: -1194.59 +Pressure step 4: 242.456, step 4: 62.96 +Vir-XX step 4: -736.257, +Reading energy frame 5 time 5.000 +Reading energy frame 5 time 0.500 +Reading energy frame 6 time 7.000 +Reading energy frame 6 time 0.600 +Reading energy frame 7 time 8.000 +Reading energy frame 7 time 0.700 +Reading energy frame 8 time 10.000 +Reading energy frame 8 time 0.800 +Reading energy frame 9 time 12.000 +Reading energy frame 9 time 0.900 +Reading energy frame 10 time 14.000 +Reading energy frame 10 time 1.000 step 4: -3.54811 +t (5.000000e+00 - 5.000000e-01) +step (5 - 250) +Angle step 5: 92.7917, step 5: 228.041 +Proper Dih. step 5: 46.4461, step 5: 11.5992 +Ryckaert-Bell. step 5: 53.249, step 5: 93.8753 +Coulomb-14 step 5: 48.2479, step 5: 114.191 +LJ (SR) step 5: -18.7401, step 5: 69.11 +Coulomb (SR) step 5: -1763.71, step 5: -2209.02 +Coul. recip. step 5: 923.209, step 5: 341.94 +Potential step 5: -341.667, step 5: -1229.05 +Pressure step 5: 356.299, step 5: 17.7417 +Vir-XX step 5: -534.09, step 5: -113.967 +t (7.000000e+00 - 6.000000e-01) +step (7 - 300) +Angle step 7: 130.86, step 7: 193.185 +Proper Dih. step 7: 42.6816, step 7: 7.0615 +Ryckaert-Bell. step 7: 53.3748, step 7: 106.945 +Coulomb-14 step 7: 49.9217, step 7: 100.896 +LJ (SR) step 7: -15.5538, step 7: 10.2121 +Coulomb (SR) step 7: -1764.3, step 7: -2143.78 +Coul. recip. step 7: 924.347, step 7: 311.339 +Potential step 7: -444.809, step 7: -1304.87 +Pressure step 7: 215.786, step 7: -61.3894 +Vir-XX step 7: -589.888, step 7: 192.034 +t (8.000000e+00 - 7.000000e-01) +step (8 - 350) +Angle step 8: 68.783, step 8: 187.181 +Proper Dih. step 8: 30.5271, step 8: 10.9997 +Ryckaert-Bell. step 8: 49.841, step 8: 123.72 +Coulomb-14 step 8: 51.1761, step 8: 123.582 +LJ (SR) step 8: -24.7767, step 8: 48.0457 +Coulomb (SR) step 8: -1761.91, step 8: -2227.32 +Coul. recip. step 8: 918.219, step 8: 267.376 +Potential step 8: -447.838, step 8: -1356 +Pressure step 8: 255.303, step 8: -36.2835 +Vir-XX step 8: -410.784, step 8: 5.87002 +t (1.000000e+01 - 8.000000e-01) +step (10 - 400) +Angle step 10: 90.876, step 10: 150.124 +Proper Dih. step 10: 26.773, step 10: 15.4228 +Ryckaert-Bell. step 10: 49.7648, step 10: 116.734 +Coulomb-14 step 10: 52.0739, step 10: 120.921 +LJ (SR) step 10: -24.2058, step 10: 61.3815 +Coulomb (SR) step 10: -1762.32, step 10: -2208.19 +Coul. recip. step 10: 918.133, step 10: 281.327 +Potential step 10: -522.879, step 10: -1339 +Pressure step 10: 177.827, step 10: 95.8529 +Vir-XX step 10: -466.151, step 10: 18.0131 +t (1.200000e+01 - 9.000000e-01) +step (12 - 450) +Angle step 12: 71.9619, step 12: 218.415 +Proper Dih. step 12: 20.7858, step 12: 6.46661 +Ryckaert-Bell. step 12: 48.0374, step 12: 118.772 +LJ-14 step 12: 113.003, step 12: 125.421 +Coulomb-14 step 12: 53.485, step 12: 111.128 +LJ (SR) step 12: -27.637, step 12: 39.4093 +Coulomb (SR) step 12: -1762.36, step 12: -2201.92 +Coul. recip. step 12: 915.934, step 12: 272.022 +Potential step 12: -542.18, step 12: -1310.71 +Pressure step 12: 180.996, step 12: -77.3705 +Vir-XX step 12: -403.068, step 12: -3.89205 +t (1.400000e+01 - 1.000000e+00) +step (14 - 500) +Angle step 14: 77.708, step 14: 188.913 +Proper Dih. step 14: 16.917, step 14: 13.1638 +Ryckaert-Bell. step 14: 47.5084, step 14: 116.045 +LJ-14 step 14: 112.831, step 14: 128.155 +Coulomb-14 step 14: 54.3835, step 14: 112.113 +LJ (SR) step 14: -29.3721, step 14: 18.6406 +Coulomb (SR) step 1 +Reading energy frame 11 time 15.000 +Last energy frame read 10 time 1.000 +GROMACS reminds you: "I do not believe continuum electrostatics" (Arieh Warshel, Nobel lecture 2013) + +4: -1762.94, step 14: -2187.48 +Coul. recip. step 14: 914.559, step 14: 304.201 +Potential step 14: -557.441, step 14: -1306.67 +Pressure step 14: 144.996, step 14: -10.3104 +Vir-XX step 14: -396.739, step 14: 362.156 + +End of file on ./ener2.edr but not on ./ener1.edr diff -r 04abdf96978b -r 17c12d5cb336 test-data/check_compare_topology.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_compare_topology.txt Tue Jul 12 12:44:22 2022 +0000 @@ -0,0 +1,287 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -s1 ./top1.tpr -s2 ./top2.tpr -abstol 0.1 + +Note: When comparing run input files, default tolerances are reduced. +Reading file ./top1.tpr, VERSION 2019.1 (single precision) +Note: file tpx version 116, software tpx version 127 +Reading file ./top2.tpr, VERSION 2022-conda_forge (single precision) +comparing inputrec +inputrec->bContinuation (0 - 1) +inputrec->epc (No - Parrinello-Rahman) +inputrec->tau_p (1.000000e+00 - 2.000000e+00) +inputrec->ref_p(x) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 1.00000e+00 0.00000e+00 0.00000e+00) +inputrec->ref_p(y) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 1.00000e+00 0.00000e+00) +inputrec->ref_p(z) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 0.00000e+00 1.00000e+00) +refcoord_scaling (COM - No) +inputrec->posres_com ( 4.98028e-01 4.93806e-01 5.09595e-01) - ( 0.00000e+00 0.00000e+00 0.00000e+00) +inputrec->posres_comB ( 4.98028e-01 4.93806e-01 5.09595e-01) - ( 0.00000e+00 0.00000e+00 0.00000e+00) +inputrec->ld_seed (-1065163585 - -1245840145) +comparing mtop topology +comparing force field parameters +numTypes (238 - 195) +ffparams->functype[181][181] (52 - 62) +ffparams->iparams[181]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[181]2: pos0A=( 1.01000004e-01, 1.01000004e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[182][182] (52 - 62) +ffparams->iparams[182]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[182]2: pos0A=( 1.47100002e-01, 1.47100002e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[183][183] (52 - 62) +ffparams->iparams[183]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[183]2: pos0A=( 1.08999997e-01, 1.08999997e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[184][184] (52 - 62) +ffparams->iparams[184]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[184]2: pos0A=( 1.52899995e-01, 1.52899995e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[185][185] (52 - 62) +ffparams->iparams[185]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[185]2: pos0A=( 1.52199998e-01, 1.52199998e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[186][186] (52 - 62) +ffparams->iparams[186]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[186]2: pos0A=( 1.22900002e-01, 1.22900002e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[187][187] (52 - 62) +ffparams->iparams[187]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[187]2: pos0A=( 1.33499995e-01, 1.33499995e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[188][188] (52 - 62) +ffparams->iparams[188]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[188]2: pos0A=( 1.44899994e-01, 1.44899994e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[189][189] (52 - 62) +ffparams->iparams[189]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[189]2: pos0A=( 1.50999993e-01, 1.50999993e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[190][190] (52 - 62) +ffparams->iparams[190]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[190]2: pos0A=( 1.40000001e-01, 1.40000001e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[191][191] (52 - 62) +ffparams->iparams[191]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[191]2: pos0A=( 1.08000003e-01, 1.08000003e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[192][192] (52 - 62) +ffparams->iparams[192]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[192]2: pos0A=( 1.46300003e-01, 1.46300003e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[193][193] (52 - 62) +ffparams->iparams[193]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[193]2: pos0A=( 1.34000003e-01, 1.34000003e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[194][194] (52 - 62) +ffparams->iparams[194]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[194]2: pos0A=( 1.25000000e-01, 1.25000000e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +comparing molecule types +comparing atoms +comparing t_resinfo +comparing t_resinfo +comparing t_resinfo +comparing t_resinfo +comparing t_resinfo +comparing InteractionLists +InteractionList size[52] (86 - 0) +InteractionList entry[0] (224 - 181) +InteractionList entry[3] (224 - 181) +InteractionList entry[6] (224 - 181) +InteractionList entry[9] (225 - 182) +InteractionList entry[12] (226 - 183) +InteractionList entry[15] (227 - 184) +InteractionList entry[18] (228 - 185) +InteractionList entry[21] (226 - 183) +InteractionList entry[24] (226 - 183) +InteractionList entry[27] (227 - 184) +InteractionList entry[30] (226 - 183) +InteractionList entry[33] (226 - 183) +InteractionList entry[36] (227 - 184) +InteractionList entry[39] (226 - 183) +InteractionList entry[42] (226 - 183) +InteractionList entry[45] (227 - 184) +InteractionList entry[48] (226 - 183) +InteractionList entry[51] (226 - 183) +InteractionList entry[54] (225 - 182) +InteractionList entry[57] (224 - 181) +InteractionList entry[60] (224 - 181) +InteractionList entry[63] (224 - 181) +InteractionList entry[66] (229 - 186) +InteractionList entry[69] (230 - 187) +InteractionList entry[72] (224 - 181) +InteractionList entry[75] (231 - 188) +InteractionList entry[78] (226 - 183) +InteractionList entry[81] (227 - 184) +InteractionList entry[84] (228 - 185) +InteractionList entry[87] (226 - 183) +InteractionList entry[90] (227 - 184) +InteractionList entry[93] (227 - 184) +InteractionList entry[96] (226 - 183) +InteractionList entry[99] (226 - 183) +InteractionList entry[102] (226 - 183) +InteractionList entry[105] (226 - 183) +InteractionList entry[108] (226 - 183) +InteractionList entry[111] (226 - 183) +InteractionList entry[114] (229 - 186) +InteractionList entry[117] (230 - 187) +InteractionList entry[120] (224 - 181) +InteractionList entry[123] (231 - 188) +InteractionList entry[126] (226 - 183) +InteractionList entry[129] (227 - 184) +InteractionList entry[132] (228 - 185) +InteractionList entry[135] (226 - 183) +InteractionList entry[138] (226 - 183) +InteractionList entry[141] (232 - 189) +InteractionList entry[144] (233 - 190) +InteractionList entry[147] (233 - 190) +InteractionList entry[150] (234 - 191) +InteractionList entry[153] (233 - 190) +InteractionList entry[156] (234 - 191) +InteractionList entry[159] (233 - 190) +InteractionList entry[162] (234 - 191) +InteractionList entry[165] (233 - 190) +InteractionList entry[168] (234 - 191) +InteractionList entry[171] (233 - 190) +InteractionList entry[174] (234 - 191) +InteractionList entry[177] (229 - 186) +InteractionList entry[180] (230 - 187) +InteractionList entry[183] (224 - 181) +InteractionList entry[186] (231 - 188) +InteractionList entry[189] (226 - 183) +InteractionList entry[192] (226 - 183) +InteractionList entry[195] (228 - 185) +InteractionList entry[198] (229 - 186) +InteractionList entry[201] (230 - 187) +InteractionList entry[204] (224 - 181) +InteractionList entry[207] (231 - 188) +InteractionList entry[210] (226 - 183) +InteractionList entry[213] (227 - 184) +InteractionList entry[216] (228 - 185) +InteractionList entry[219] (226 - 183) +InteractionList entry[222] (226 - 183) +InteractionList entry[225] (227 - 184) +InteractionList entry[228] (226 - 183) +InteractionList entry[231] (226 - 183) +InteractionList entry[234] (227 - 184) +InteractionList entry[237] (226 - 183) +InteractionList entry[240] (226 - 183) +InteractionList entry[243] (235 - 192) +InteractionList entry[246] (224 - 181) +InteractionList entry[249] (236 - 193) +InteractionList entry[252] (236 - 193) +InteractionList entry[255] (236 - 193) +InteractionList entry[258] (224 - 181) +InteractionList entry[261] (224 - 181) +InteractionList entry[264] (224 - 181) +InteractionList entry[267] (224 - 181) +InteractionList entry[270] (237 - 194) +InteractionList entry[273] (237 - 194) +comparing blocka excls[0] +comparing atoms +comparing t_resinfo +comparing InteractionLists +comparing blocka excls[1] +comparing molecule blocks +posres_xA size[0] (92 - 0) +posres_xB size[0] (92 - 0) +comparing InteractionLists +comparing atomtypes +comparing groups +comparing intermolecular exclusions +comparing moleculeBlockIndices +comparing flags +comparing box +comparing box_rel +box_rel[ 1] ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 1.00000e+00 0.00000e+00) +box_rel[ 2] ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 0.00000e+00 1.00000e+00) +comparing boxv +comparing x +x[ 0] ( 2.08100e+00 2.64900e+00 1.48700e+00) - ( 2.00500e+00 2.65900e+00 1.53400e+00) +x[ 1] ( 2.15700e+00 2.70300e+00 1.44900e+00) - ( 2.04100e+00 2.72300e+00 1.46500e+00) +x[ 2] ( 2.01500e+00 2.62900e+00 1.41500e+00) - ( 1.91500e+00 2.62200e+00 1.50600e+00) +x[ 3] ( 2.03700e+00 2.70100e+00 1.56000e+00) - ( 1.98500e+00 2.70300e+00 1.62200e+00) +x[ 4] ( 2.13400e+00 2.52200e+00 1.54200e+00) - ( 2.09200e+00 2.54200e+00 1.55500e+00) +x[ 5] ( 2.17800e+00 2.47000e+00 1.46900e+00) - ( 2.11500e+00 2.49900e+00 1.45800e+00) +x[ 6] ( 2.23200e+00 2.55900e+00 1.65400e+00) - ( 2.22300e+00 2.57600e+00 1.62600e+00) +x[ 7] ( 2.30800e+00 2.61000e+00 1.61500e+00) - ( 2.28400e+00 2.63700e+00 1.56000e+00) +x[ 8] ( 2.18400e+00 2.61600e+00 1.72100e+00) - ( 2.19900e+00 2.64400e+00 1.70800e+00) +x[ 9] ( 2.29000e+00 2.44000e+00 1.72900e+00) - ( 2.30300e+00 2.45700e+00 1.67800e+00) +x[ 10] ( 2.22100e+00 2.40400e+00 1.79100e+00) - ( 2.23700e+00 2.37200e+00 1.69400e+00) +x[ 11] ( 2.31500e+00 2.36900e+00 1.66200e+00) - ( 2.37500e+00 2.42200e+00 1.60400e+00) +x[ 12] ( 2.41400e+00 2.48000e+00 1.80800e+00) - ( 2.36400e+00 2.47300e+00 1.81800e+00) +x[ 13] ( 2.49000e+00 2.49800e+00 1.74500e+00) - ( 2.44000e+00 2.55000e+00 1.80900e+00) +x[ 14] ( 2.39400e+00 2.56200e+00 1.86100e+00) - ( 2.28500e+00 2.51300e+00 1.88200e+00) +x[ 15] ( 2.45100e+00 2.36600e+00 1.90100e+00) - ( 2.41900e+00 2.34700e+00 1.88500e+00) +x[ 16] ( 2.38600e+00 2.36100e+00 1.97700e+00) - ( 2.34100e+00 2.27200e+00 1.89600e+00) +x[ 17] ( 2.45100e+00 2.27900e+00 1.85200e+00) - ( 2.50100e+00 2.30900e+00 1.82400e+00) +x[ 18] ( 2.58700e+00 2.39200e+00 1.95500e+00) - ( 2.47900e+00 2.37600e+00 2.01600e+00) +x[ 19] ( 2.61400e+00 2.31800e+00 2.01700e+00) - ( 2.50700e+00 2.28900e+00 2.06000e+00) +x[ 20] ( 2.65300e+00 2.39700e+00 1.87900e+00) - ( 2.56100e+00 2.43400e+00 2.00300e+00) +x[ 21] ( 2.58700e+00 2.47900e+00 2.00500e+00) - ( 2.41200e+00 2.42000e+00 2.07700e+00) +x[ 22] ( 2.01900e+00 2.44100e+00 1.60100e+00) - ( 2.00300e+00 2.44500e+00 1.63200e+00) +x[ 23] ( 1.94000e+00 2.49600e+00 1.67700e+00) - ( 1.94900e+00 2.48400e+00 1.73500e+00) +x[ 24] ( 2.01900e+00 2.31100e+00 1.58100e+00) - ( 1.98900e+00 2.32100e+00 1.58600e+00) +x[ 25] ( 2.08100e+00 2.27500e+00 1.51100e+00) - ( 2.04300e+00 2.28700e+00 1.50700e+00) +x[ 26] ( 1.93500e+00 2.21500e+00 1.65200e+00) - ( 1.91500e+00 2.22000e+00 1.65900e+00) +x[ 27] ( 1.86200e+00 2.26700e+00 1.69500e+00) - ( 1.82800e+00 2.26100e+00 1.71100e+00) +x[ 28] ( 1.85900e+00 2.11800e+00 1.56200e+00) - ( 1.87000e+00 2.11800e+00 1.55400e+00) +x[ 29] ( 1.93100e+00 2.06700e+00 1.51500e+00) - ( 1.95500e+00 2.06400e+00 1.51500e+00) +x[ 30] ( 1.77000e+00 2.02300e+00 1.64200e+00) - ( 1.76700e+00 2.01600e+00 1.60300e+00) +x[ 31] ( 1.72200e+00 1.96200e+00 1.57900e+00) - ( 1.74100e+00 1.94000e+00 1.52900e+00) +x[ 32] ( 1.82700e+00 1.97000e+00 1.70400e+00) - ( 1.80800e+00 1.96600e+00 1.69100e+00) +x[ 33] ( 1.70300e+00 2.07600e+00 1.69400e+00) - ( 1.67500e+00 2.06400e+00 1.63600e+00) +x[ 34] ( 1.77400e+00 2.18600e+00 1.45600e+00) - ( 1.80000e+00 2.18700e+00 1.43700e+00) +x[ 35] ( 1.72800e+00 2.11700e+00 1.40100e+00) - ( 1.73400e+00 2.12700e+00 1.37500e+00) +x[ 36] ( 1.70700e+00 2.24500e+00 1.50000e+00) - ( 1.74500e+00 2.27400e+00 1.47400e+00) +x[ 37] ( 1.83300e+00 2.24200e+00 1.39700e+00) - ( 1.87800e+00 2.22700e+00 1.37200e+00) +x[ 38] ( 2.02500e+00 2.14600e+00 1.75600e+00) - ( 2.01800e+00 2.16000e+00 1.75400e+00) +x[ 39] ( 2.12100e+00 2.07600e+00 1.71900e+00) - ( 2.12800e+00 2.11900e+00 1.71700e+00) +x[ 40] ( 1.99400e+00 2.17000e+00 1.88100e+00) - ( 1.98500e+00 2.15700e+00 1.88300e+00) +x[ 41] ( 1.92000e+00 2.23400e+00 1.90100e+00) - ( 1.88700e+00 2.15500e+00 1.90700e+00) +x[ 42] ( 2.06400e+00 2.10500e+00 1.99300e+00) - ( 2.07100e+00 2.10500e+00 1.98700e+00) +x[ 43] ( 2.16000e+00 2.11200e+00 1.96800e+00) - ( 2.17800e+00 2.09600e+00 1.96500e+00) +x[ 44] ( 2.04200e+00 2.17800e+00 2.12600e+00) - ( 2.04500e+00 2.17600e+00 2.12000e+00) +x[ 45] ( 1.95000e+00 2.21700e+00 2.12700e+00) - ( 1.94300e+00 2.21300e+00 2.12000e+00) +x[ 46] ( 2.05100e+00 2.11300e+00 2.20100e+00) - ( 2.04300e+00 2.11500e+00 2.21000e+00) +x[ 47] ( 2.13900e+00 2.28900e+00 2.14700e+00) - ( 2.14100e+00 2.29000e+00 2.14800e+00) +x[ 48] ( 2.11200e+00 2.42000e+00 2.10500e+00) - ( 2.12300e+00 2.41300e+00 2.08400e+00) +x[ 49] ( 2.02600e+00 2.44000e+00 2.05800e+00) - ( 2.04900e+00 2.42000e+00 2.00600e+00) +x[ 50] ( 2.24500e+00 2.27100e+00 2.23800e+00) - ( 2.23700e+00 2.27100e+00 2.24800e+00) +x[ 51] ( 2.25800e+00 2.18100e+00 2.28000e+00) - ( 2.25000e+00 2.17500e+00 2.29600e+00) +x[ 52] ( 2.20300e+00 2.52300e+00 2.12800e+00) - ( 2.19200e+00 2.52400e+00 2.13400e+00) +x[ 53] ( 2.19300e+00 2.61000e+00 2.08100e+00) - ( 2.17400e+00 2.62100e+00 2.09100e+00) +x[ 54] ( 2.33200e+00 2.37400e+00 2.26900e+00) - ( 2.30700e+00 2.38200e+00 2.29600e+00) +x[ 55] ( 2.41100e+00 2.35700e+00 2.32800e+00) - ( 2.37800e+00 2.36900e+00 2.37600e+00) +x[ 56] ( 2.30900e+00 2.50200e+00 2.21800e+00) - ( 2.28200e+00 2.50800e+00 2.24000e+00) +x[ 57] ( 2.36700e+00 2.57900e+00 2.24600e+00) - ( 2.33500e+00 2.59400e+00 2.27800e+00) +x[ 58] ( 2.01900e+00 1.95900e+00 2.00800e+00) - ( 2.03500e+00 1.96000e+00 2.01800e+00) +x[ 59] ( 1.89700e+00 1.93100e+00 1.99900e+00) - ( 1.93600e+00 1.90800e+00 1.96700e+00) +x[ 60] ( 2.11700e+00 1.87900e+00 2.05200e+00) - ( 2.11600e+00 1.89700e+00 2.10300e+00) +x[ 61] ( 2.21200e+00 1.91000e+00 2.05300e+00) - ( 2.17200e+00 1.95000e+00 2.16800e+00) +x[ 62] ( 2.08200e+00 1.74300e+00 2.09800e+00) - ( 2.08300e+00 1.76000e+00 2.13800e+00) +x[ 63] ( 2.00700e+00 1.70700e+00 2.04200e+00) - ( 2.01900e+00 1.70400e+00 2.06900e+00) +x[ 64] ( 2.16100e+00 1.68300e+00 2.09100e+00) - ( 2.17700e+00 1.71100e+00 2.16100e+00) +x[ 65] ( 2.03700e+00 1.75700e+00 2.24300e+00) - ( 2.00800e+00 1.78300e+00 2.26900e+00) +x[ 66] ( 2.07500e+00 1.85500e+00 2.30700e+00) - ( 1.98300e+00 1.89000e+00 2.32300e+00) +x[ 67] ( 1.95000e+00 1.66900e+00 2.28800e+00) - ( 1.96400e+00 1.67400e+00 2.33300e+00) +x[ 68] ( 1.91600e+00 1.59900e+00 2.22500e+00) - ( 2.00100e+00 1.58400e+00 2.30700e+00) +x[ 69] ( 1.90100e+00 1.66900e+00 2.42600e+00) - ( 1.90200e+00 1.66500e+00 2.46400e+00) +x[ 70] ( 1.84300e+00 1.74900e+00 2.43300e+00) - ( 1.85200e+00 1.75700e+00 2.49300e+00) +x[ 71] ( 1.82100e+00 1.54100e+00 2.45200e+00) - ( 1.79000e+00 1.56300e+00 2.44200e+00) +x[ 72] ( 1.74500e+00 1.53700e+00 2.38800e+00) - ( 1.76700e+00 1.56100e+00 2.33500e+00) +x[ 73] ( 1.88100e+00 1.46200e+00 2.43800e+00) - ( 1.82100e+00 1.46000e+00 2.45400e+00) +x[ 74] ( 1.76600e+00 1.53500e+00 2.59300e+00) - ( 1.68200e+00 1.57700e+00 2.54900e+00) +x[ 75] ( 1.84200e+00 1.53200e+00 2.65800e+00) - ( 1.65100e+00 1.68000e+00 2.56200e+00) +x[ 76] ( 1.71000e+00 1.61600e+00 2.61000e+00) - ( 1.58800e+00 1.54200e+00 2.50700e+00) +x[ 77] ( 1.68300e+00 1.41500e+00 2.61300e+00) - ( 1.70700e+00 1.49400e+00 2.67500e+00) +x[ 78] ( 1.64900e+00 1.41400e+00 2.70700e+00) - ( 1.77900e+00 1.52800e+00 2.75000e+00) +x[ 79] ( 1.60500e+00 1.42000e+00 2.55000e+00) - ( 1.61600e+00 1.49900e+00 2.73500e+00) +x[ 80] ( 1.75100e+00 1.29000e+00 2.58900e+00) - ( 1.73200e+00 1.35300e+00 2.64800e+00) +x[ 81] ( 1.74700e+00 1.25500e+00 2.49600e+00) - ( 1.64100e+00 1.31200e+00 2.63200e+00) +x[ 82] ( 1.81800e+00 1.21600e+00 2.67500e+00) - ( 1.83600e+00 1.27300e+00 2.67800e+00) +x[ 83] ( 1.82900e+00 1.24800e+00 2.80400e+00) - ( 1.94600e+00 1.33800e+00 2.71700e+00) +x[ 84] ( 1.78400e +GROMACS reminds you: "Pain is inevitable. Suffering is optional." (Haruki Murakami) + ++00 1.33100e+00 2.83800e+00) - ( 1.94400e+00 1.43900e+00 2.72300e+00) +x[ 85] ( 1.88100e+00 1.19000e+00 2.86600e+00) - ( 2.03900e+00 1.29700e+00 2.71100e+00) +x[ 86] ( 1.87000e+00 1.09900e+00 2.63200e+00) - ( 1.83400e+00 1.14000e+00 2.66600e+00) +x[ 87] ( 1.85600e+00 1.07000e+00 2.53800e+00) - ( 1.75700e+00 1.09400e+00 2.62000e+00) +x[ 88] ( 1.92100e+00 1.04100e+00 2.69500e+00) - ( 1.90200e+00 1.08100e+00 2.71200e+00) +x[ 89] ( 2.01200e+00 1.68800e+00 2.52900e+00) - ( 2.00200e+00 1.59300e+00 2.55400e+00) +x[ 90] ( 2.01200e+00 1.78000e+00 2.61500e+00) - ( 1.96600e+00 1.60300e+00 2.67300e+00) +x[ 91] ( 1.97500e+00 1.68900e+00 2.66000e+00) - ( 2.09800e+00 1.52500e+00 2.51200e+00) +x[ 92] ( 8.65000e-01 2.21000e+00 2.05700e+00) - ( 1.57100e+00 2.29900e+00 1.78700e+00) +x[ 93] ( 2.87900e+00 3.76300e+00 2.61500e+00) - ( 2.64400e+00 3.40800e+00 2.32600e+00) +comparing v diff -r 04abdf96978b -r 17c12d5cb336 test-data/check_compare_traj.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_compare_traj.txt Tue Jul 12 12:44:22 2022 +0000 @@ -0,0 +1,62 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/5/working +Command line: + gmx check -f ./traj1.xtc -f2 ./traj2.xtc -rmsd -tol 0.1 -abstol 0.1 + +Comparing trajectory files ./traj1.xtc and ./traj2.xtc + +Reading frame 0 time 0.000 +Reading frame 0 time 0.000 +Reading frame 1 time 0.100 +Reading frame 1 time 0.100 +Reading frame 2 time 0.200 +Reading frame 2 time 0.200 +Reading frame 3 time 0.300 +Reading frame 3 time 0.300 +Reading frame 4 time 0.400 +Reading frame 4 time 0.400 +Reading frame 5 time 0.500 +Reading frame 5 time 0.500 +Reading frame 6 time 0.600 +Reading frame 6 time 0.600 +Reading frame 7 time 0.700 +Reading frame 7 time 0.700 +Reading frame 8 time 0.800 +Reading frame 8 time 0.800 +Reading frame 9 time 0.900 +Reading frame 9 time 0.900 +Reading frame 10 time 1.000 +Reading frame 10 time 1.000 +Last frame 10 time 1.000 + +Last frame 10 time 1.000 + +GROMACS reminds you: "As always in life, people want a simple answer... and it's always wrong." (Marie Daly) + + +x RMSD 0.135353 + +x RMSD 0.150079 + +x RMSD 0.161998 + +x RMSD 0.186695 + +x RMSD 0.201164 + +x RMSD 0.222255 + +x RMSD 0.242077 + +x RMSD 0.259343 + +x RMSD 0.260618 + +x RMSD 0.256508 + +x RMSD 0.256135 + +Both files read correctly diff -r 04abdf96978b -r 17c12d5cb336 test-data/check_info_energy.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_info_energy.txt Tue Jul 12 12:44:22 2022 +0000 @@ -0,0 +1,67 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -e ./ener.edr + +Checking energy file ./ener.edr + +Opened ./ener.edr as single precision energy file +31 groups in energy file +Reading energy frame 0 time 0.000 +frame: 0 (index 0), t: 0.000 + +Reading energy frame 1 time 1.000 +Reading energy frame 2 time 2.000 +Reading energy frame 3 time 3.000 +Reading energy frame 4 time 4.000 +Reading energy frame 5 time 5.000 +Reading energy frame 6 time 7.000 +Timesteps at t=5 don't match (1, 2) + +Reading energy frame 7 time 8.000 +Timesteps at t=7 don't match (2, 1) + +Reading energy frame 8 time 10.000 +Timesteps at t=8 don't match (1, 2) + +Reading energy frame 9 time 12.000 +Reading energy frame 10 time 14.000 +Reading energy frame 11 time 15.000 +Timesteps at t=14 don't match (2, 1) + +Reading energy frame 12 time 17.000 +Timesteps at t=15 don't match (1, 2) + +Reading energy frame 13 time 18.000 +Timesteps at t=17 don't match (2, 1) + +Reading energy frame 14 time 20.000 +Timesteps at t=18 don't match (1, 2) + +Reading energy frame 15 time 21.000 +Timesteps at t=20 don't match (2, 1) + +Reading energy frame 16 time 22.000 +Reading energy frame 17 time 23.000 +Reading energy frame 18 time 25.000 +Timesteps at t=23 don't match (1, 2) + +Reading energy frame 19 time 26.000 +Timesteps at t=25 don't match (2, 1) + +Reading energy frame 20 time 27.000 +Timesteps at t=28 don't match (1, 2) + +Timesteps at t=30 don't match (2, 1) + +Timesteps at t=31 don't match (1, 2) + +Last energy frame read 24 time 33.000 + +Found 25 frames. + +GROMACS reminds you: "The Lord of the Rings can be confusing to follow because many of the bad minions look and sound familiar; that's why Tolkien gave them each an ORCid." (Caroline Bartman) + diff -r 04abdf96978b -r 17c12d5cb336 test-data/check_info_index.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_info_index.txt Tue Jul 12 12:44:22 2022 +0000 @@ -0,0 +1,28 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -n ./index.ndx + + +GROMACS reminds you: "Jede der Scherben spiegelt das Licht" (Wir sind Helden) + +Contents of index file ./index.ndx +-------------------------------------------------- +Nr. Group #Entries First Last + 0 System 94 1 94 + 1 Protein 92 1 92 + 2 Protein-H 43 1 92 + 3 C-alpha 5 5 70 + 4 Backbone 15 1 90 + 5 MainChain 21 1 92 + 6 MainChain+Cb 25 1 92 + 7 MainChain+H 28 1 92 + 8 SideChain 64 6 89 + 9 SideChain-H 22 7 87 + 10 Prot-Masses 92 1 92 + 11 non-Protein 2 93 94 + 12 Ion 2 93 94 + 13 CL 2 93 94 diff -r 04abdf96978b -r 17c12d5cb336 test-data/check_info_structure.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_info_structure.txt Tue Jul 12 12:44:22 2022 +0000 @@ -0,0 +1,480 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -c ./struc.gro -vdwfac 0.8 -bonlo 0.4 -bonhi 0.7 + +Checking coordinate file ./struc.gro +94 atoms in file +coordinates found +box found +velocities absent + +Checking for atoms closer than 0.8 and not between 0.4 and 0.7, +relative to sum of Van der Waals distance: + +WARNING: Masses and atomic (Van der Waals) radii will be guessed + based on residue and atom names, since they could not be + definitively assigned from the information in your input + files. These guessed numbers might deviate from the mass + and radius of the atom type. Please check the output + files if necessary. Note, that this functionality may + be removed in a future GROMACS version. Please, consider + using another file format for your input. + + +WARNING: Masses and atomic (Van der Waals) radii will be guessed + based on residue and atom names, since they could not be + definitively assigned from the information in your input + files. These guessed numbers might deviate from the mass + and radius of the atom type. Please check the output + files if necessary. Note, that this functionality may + be removed in a future GROMACS version. Please, consider + using another file format for your input. + +NOTE: From version 5.0 gmx check uses the Van der Waals radii +from the source below. This means the results may be different +compared to previous GROMACS versions. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +A. Bondi +van der Waals Volumes and Radii +J. Phys. Chem. 68 (1964) pp. 441-451 +-------- -------- --- Thank You --- -------- -------- + + +atom# name residue r_vdw atom# name residue r_vdw distance + + 1 N LYS 1 0.155 2 H1 LYS 1 0.12 0.1008 + + 1 N LYS 1 0.155 3 H2 LYS 1 0.12 0.1012 + + 1 N LYS 1 0.155 4 H3 LYS 1 0.12 0.1019 + + 1 N LYS 1 0.155 6 HA LYS 1 0.12 0.2103 + + 1 N LYS 1 0.155 7 CB LYS 1 0.17 0.2447 + + 1 N LYS 1 0.155 23 C LYS 1 0.17 0.2437 + + 2 H1 LYS 1 0.12 5 CA LYS 1 0.17 0.205 + + 3 H2 LYS 1 0.12 5 CA LYS 1 0.17 0.204 + + 5 CA LYS 1 0.17 6 HA LYS 1 0.12 0.1093 + + 5 CA LYS 1 0.17 8 HB1 LYS 1 0.12 0.2166 + + 5 CA LYS 1 0.17 9 HB2 LYS 1 0.12 0.2169 + + 5 CA LYS 1 0.17 10 CG LYS 1 0.17 0.2598 + + 5 CA LYS 1 0.17 24 O LYS 1 0.152 0.235 + + 5 CA LYS 1 0.17 25 N VAL 2 0.155 0.2455 + + 6 HA LYS 1 0.12 7 CB LYS 1 0.17 0.2176 + + 6 HA LYS 1 0.12 23 C LYS 1 0.17 0.215 + + 7 CB LYS 1 0.17 8 HB1 LYS 1 0.12 0.1093 + + 7 CB LYS 1 0.17 9 HB2 LYS 1 0.12 0.1089 + + 7 CB LYS 1 0.17 11 HG1 LYS 1 0.12 0.2154 + + 7 CB LYS 1 0.17 12 HG2 LYS 1 0.12 0.217 + + 7 CB LYS 1 0.17 13 CD LYS 1 0.17 0.252 + + 7 CB LYS 1 0.17 23 C LYS 1 0.17 0.2504 + + 8 HB1 LYS 1 0.12 9 HB2 LYS 1 0.12 0.1744 + + 8 HB1 LYS 1 0.12 10 CG LYS 1 0.17 0.2149 + + 9 HB2 LYS 1 0.12 10 CG LYS 1 0.17 0.2132 + + 10 + 10 CG LYS 1 0.17 11 HG1 LYS 1 0.12 0.1093 + + 10 CG LYS 1 0.17 12 HG2 LYS 1 0.12 0.1094 + + 10 CG LYS 1 0.17 14 HD1 LYS 1 0.12 0.2135 + + 10 CG LYS 1 0.17 15 HD2 LYS 1 0.12 0.2152 + + 10 CG LYS 1 0.17 16 CE LYS 1 0.17 0.251 + + 11 HG1 LYS 1 0.12 12 HG2 LYS 1 0.12 0.1752 + + 11 HG1 LYS 1 0.12 13 CD LYS 1 0.17 0.2145 + + 12 HG2 LYS 1 0.12 13 CD LYS 1 0.17 0.2141 + + 13 CD LYS 1 0.17 14 HD1 LYS 1 0.12 0.1091 + + 13 CD LYS 1 0.17 15 HD2 LYS 1 0.12 0.1097 + + 13 CD LYS 1 0.17 17 HE1 LYS 1 0.12 0.2158 + + 13 CD LYS 1 0.17 18 HE2 LYS 1 0.12 0.2161 + + 13 CD LYS 1 0.17 19 NZ LYS 1 0.155 0.2464 + + 14 HD1 LYS 1 0.12 15 HD2 LYS 1 0.12 0.1756 + + 14 HD1 LYS 1 0.12 16 CE LYS 1 0.17 0.2168 + + 15 HD2 LYS 1 0.12 16 CE LYS 1 0.17 0.2152 + + 16 CE LYS 1 0.17 17 HE1 LYS 1 0.12 0.1087 + + 16 CE LYS 1 0.17 18 HE2 LYS 1 0.12 0.1097 + + 16 CE LYS 1 0.17 20 HZ1 LYS 1 0.12 0.205 + + 16 CE LYS 1 0.17 21 HZ2 LYS 1 0.12 0.2042 + + 16 CE LYS 1 0.17 22 HZ3 LYS 1 0.12 0.2043 + + 17 HE1 LYS 1 0.12 18 HE2 LYS 1 0.12 0.1752 + + 17 HE1 LYS 1 0.12 19 NZ LYS 1 0.155 0.2104 + + 18 HE2 LYS 1 0.12 19 NZ LYS 1 0.155 0.2104 + + 19 NZ LYS 1 0.155 20 HZ1 LYS 1 0.12 0.1013 + + 19 NZ LYS 1 0.155 21 HZ2 LYS 1 0.12 0.1007 + + 19 NZ LYS 1 0.155 22 HZ3 LYS 1 0.12 0.1008 + + 20 + 23 C LYS 1 0.17 24 O LYS 1 0.152 0.1227 + + 23 C LYS 1 0.17 26 H VAL 2 0.12 0.2057 + + 23 C LYS 1 0.17 27 CA VAL 2 0.17 0.2452 + + 24 O LYS 1 0.152 25 N VAL 2 0.155 0.2265 + + 25 N VAL 2 0.155 26 H VAL 2 0.12 0.1012 + + 25 N VAL 2 0.155 28 HA VAL 2 0.12 0.212 + + 25 N VAL 2 0.155 29 CB VAL 2 0.17 0.2483 + + 25 N VAL 2 0.155 39 C VAL 2 0.17 0.2402 + + 26 H VAL 2 0.12 27 CA VAL 2 0.17 0.2099 + + 27 CA VAL 2 0.17 28 HA VAL 2 0.12 0.1087 + + 27 CA VAL 2 0.17 30 HB VAL 2 0.12 0.2176 + + 27 CA VAL 2 0.17 31 CG1 VAL 2 0.17 0.2542 + + 27 CA VAL 2 0.17 35 CG2 VAL 2 0.17 0.2536 + + 27 CA VAL 2 0.17 40 O VAL 2 0.152 0.2414 + + 27 CA VAL 2 0.17 41 N PHE 3 0.155 0.2429 + + 28 HA VAL 2 0.12 29 CB VAL 2 0.17 0.2139 + + 28 HA VAL 2 0.12 39 C VAL 2 0.17 0.2153 + + 29 CB VAL 2 0.17 30 HB VAL 2 0.12 0.1099 + + 29 CB VAL 2 0.17 32 HG11 VAL 2 0.12 0.2179 + + 29 CB VAL 2 0.17 33 HG12 VAL 2 0.12 0.2189 + + 29 CB VAL 2 0.17 34 HG13 VAL 2 0.12 0.2179 + + 29 CB VAL 2 0.17 36 HG21 VAL 2 0.12 0.2167 + + 29 CB VAL 2 0.17 37 HG22 VAL 2 0.12 0.2176 + + 29 CB VAL 2 0.17 38 HG23 VAL 2 0.12 0.2192 + + 29 CB VAL 2 0.17 39 C VAL 2 0.17 0.2543 + + 30 + 30 HB VAL 2 0.12 31 CG1 VAL 2 0.17 0.215 + + 30 HB VAL 2 0.12 35 CG2 VAL 2 0.17 0.2146 + + 31 CG1 VAL 2 0.17 32 HG11 VAL 2 0.12 0.1091 + + 31 CG1 VAL 2 0.17 33 HG12 VAL 2 0.12 0.1089 + + 31 CG1 VAL 2 0.17 34 HG13 VAL 2 0.12 0.1094 + + 31 CG1 VAL 2 0.17 35 CG2 VAL 2 0.17 0.2487 + + 32 HG11 VAL 2 0.12 33 HG12 VAL 2 0.12 0.1757 + + 32 HG11 VAL 2 0.12 34 HG13 VAL 2 0.12 0.1765 + + 33 HG12 VAL 2 0.12 34 HG13 VAL 2 0.12 0.1761 + + 35 CG2 VAL 2 0.17 36 HG21 VAL 2 0.12 0.1084 + + 35 CG2 VAL 2 0.17 37 HG22 VAL 2 0.12 0.1092 + + 35 CG2 VAL 2 0.17 38 HG23 VAL 2 0.12 0.1092 + + 36 HG21 VAL 2 0.12 37 HG22 VAL 2 0.12 0.176 + + 36 HG21 VAL 2 0.12 38 HG23 VAL 2 0.12 0.1755 + + 37 HG22 VAL 2 0.12 38 HG23 VAL 2 0.12 0.1767 + + 39 C VAL 2 0.17 40 O VAL 2 0.152 0.1239 + + 39 C VAL 2 0.17 43 CA PHE 3 0.17 0.2449 + + 40 + 40 O VAL 2 0.152 41 N PHE 3 0.155 0.226 + + 41 N PHE 3 0.155 42 H PHE 3 0.12 0.1006 + + 41 N PHE 3 0.155 44 HA PHE 3 0.12 0.2084 + + 41 N PHE 3 0.155 45 CB PHE 3 0.17 0.2467 + + 41 N PHE 3 0.155 59 C PHE 3 0.17 0.2453 + + 42 H PHE 3 0.12 43 CA PHE 3 0.17 0.2117 + + 43 CA PHE 3 0.17 44 HA PHE 3 0.12 0.109 + + 43 CA PHE 3 0.17 46 HB1 PHE 3 0.12 0.2198 + + 43 CA PHE 3 0.17 47 HB2 PHE 3 0.12 0.2178 + + 43 CA PHE 3 0.17 48 CG PHE 3 0.17 0.2554 + + 43 CA PHE 3 0.17 60 O PHE 3 0.152 0.2405 + + 43 CA PHE 3 0.17 61 N GLY 4 0.155 0.2431 + + 44 HA PHE 3 0.12 45 CB PHE 3 0.17 0.2178 + + 44 HA PHE 3 0.12 59 C PHE 3 0.17 0.2144 + + 45 CB PHE 3 0.17 46 HB1 PHE 3 0.12 0.109 + + 45 CB PHE 3 0.17 47 HB2 PHE 3 0.12 0.1089 + + 45 CB PHE 3 0.17 49 CD1 PHE 3 0.17 0.2542 + + 45 CB PHE 3 0.17 51 CD2 PHE 3 0.17 0.2528 + + 45 CB PHE 3 0.17 59 C PHE 3 0.17 0.2487 + + 46 HB1 PHE 3 0.12 47 HB2 PHE 3 0.12 0.1734 + + 46 HB1 PHE 3 0.12 48 CG PHE 3 0.17 0.2139 + + 47 HB2 PHE 3 0.12 48 CG PHE 3 0.17 0.2104 + + 48 CG PHE 3 0.17 50 HD1 PHE 3 0.12 0.2158 + + 48 CG PHE 3 0.17 52 HD2 PHE 3 0.12 0.2172 + + 48 CG PHE 3 0.17 53 CE1 PHE 3 0.17 0.2437 + + 48 CG PHE 3 0.17 55 CE2 PHE 3 0.17 0.2448 + + 49 CD1 PHE 3 0.17 50 HD1 PHE 3 0.12 0.1082 + + 49 CD1 PHE 3 0.17 51 CD2 PHE 3 0.17 0.244 + + 49 CD1 PHE 3 0.17 54 HE1 PHE 3 0.12 0.2153 + + 49 CD1 PHE 3 0.17 57 CZ PHE 3 0.17 0.2436 + + 50 + 50 HD1 PHE 3 0.12 53 CE1 PHE 3 0.17 0.2161 + + 51 CD2 PHE 3 0.17 52 HD2 PHE 3 0.12 0.1089 + + 51 CD2 PHE 3 0.17 56 HE2 PHE 3 0.12 0.2157 + + 51 CD2 PHE 3 0.17 57 CZ PHE 3 0.17 0.2439 + + 52 HD2 PHE 3 0.12 55 CE2 PHE 3 0.17 0.2171 + + 53 CE1 PHE 3 0.17 54 HE1 PHE 3 0.12 0.108 + + 53 CE1 PHE 3 0.17 55 CE2 PHE 3 0.17 0.2446 + + 53 CE1 PHE 3 0.17 58 HZ PHE 3 0.12 0.216 + + 54 HE1 PHE 3 0.12 57 CZ PHE 3 0.17 0.2166 + + 55 CE2 PHE 3 0.17 56 HE2 PHE 3 0.12 0.1079 + + 55 CE2 PHE 3 0.17 58 HZ PHE 3 0.12 0.2152 + + 56 HE2 PHE 3 0.12 57 CZ PHE 3 0.17 0.2174 + + 57 CZ PHE 3 0.17 58 HZ PHE 3 0.12 0.1074 + + 59 C PHE 3 0.17 60 O PHE 3 0.152 0.1233 + + 59 C PHE 3 0.17 63 CA GLY 4 0.17 0.2439 + + 60 + 60 O PHE 3 0.152 61 N GLY 4 0.155 0.2261 + + 61 N GLY 4 0.155 62 H GLY 4 0.12 0.1014 + + 61 N GLY 4 0.155 64 HA1 GLY 4 0.12 0.2097 + + 61 N GLY 4 0.155 65 HA2 GLY 4 0.12 0.208 + + 61 N GLY 4 0.155 66 C GLY 4 0.17 0.2418 + + 62 H GLY 4 0.12 63 CA GLY 4 0.17 0.2113 + + 63 CA GLY 4 0.17 64 HA1 GLY 4 0.12 0.109 + + 63 CA GLY 4 0.17 65 HA2 GLY 4 0.12 0.1096 + + 63 CA GLY 4 0.17 67 O GLY 4 0.152 0.2357 + + 63 CA GLY 4 0.17 68 N ARG 5 0.155 0.2453 + + 64 HA1 GLY 4 0.12 65 HA2 GLY 4 0.12 0.1769 + + 64 HA1 GLY 4 0.12 66 C GLY 4 0.17 0.2199 + + 65 HA2 GLY 4 0.12 66 C GLY 4 0.17 0.214 + + 66 C GLY 4 0.17 67 O GLY 4 0.152 0.1224 + + 66 C GLY 4 0.17 70 CA ARG 5 0.17 0.2528 + + 67 O GLY 4 0.152 68 N ARG 5 0.155 0.2269 + + 68 N ARG 5 0.155 69 H ARG 5 0.12 0.1006 + + 68 N ARG 5 0.155 71 HA ARG 5 0.12 0.2006 + + 68 N ARG 5 0.155 72 CB ARG 5 0.17 0.2455 + + 69 H ARG 5 0.12 70 CA ARG 5 0.17 0.2121 + + 70 + 70 CA ARG 5 0.17 71 HA ARG 5 0.12 0.1085 + + 70 CA ARG 5 0.17 73 HB1 ARG 5 0.12 0.217 + + 70 CA ARG 5 0.17 74 HB2 ARG 5 0.12 0.2158 + + 70 CA ARG 5 0.17 75 CG ARG 5 0.17 0.2571 + + 70 CA ARG 5 0.17 91 O1 ARG 5 0.152 0.2432 + + 70 CA ARG 5 0.17 92 O2 ARG 5 0.152 0.2442 + + 71 HA ARG 5 0.12 72 CB ARG 5 0.17 0.2124 + + 71 HA ARG 5 0.12 90 C ARG 5 0.17 0.2062 + + 72 CB ARG 5 0.17 73 HB1 ARG 5 0.12 0.1104 + + 72 CB ARG 5 0.17 74 HB2 ARG 5 0.12 0.1091 + + 72 CB ARG 5 0.17 76 HG1 ARG 5 0.12 0.2188 + + 72 CB ARG 5 0.17 77 HG2 ARG 5 0.12 0.2156 + + 72 CB ARG 5 0.17 78 CD ARG 5 0.17 0.2564 + + 72 CB ARG 5 0.17 90 C ARG 5 0.17 0.2656 + + 73 HB1 ARG 5 0.12 74 HB2 ARG 5 0.12 0.1759 + + 73 HB1 ARG 5 0.12 75 CG ARG 5 0.17 0.2148 + + 74 HB2 ARG 5 0.12 75 CG ARG 5 0.17 0.217 + + 75 CG ARG 5 0.17 76 HG1 ARG 5 0.12 0.1079 + + 75 CG ARG 5 0.17 77 HG2 ARG 5 0.12 0.1091 + + 75 CG ARG 5 0.17 79 HD1 ARG 5 0.12 0.2096 + + 75 CG ARG 5 0.17 80 HD2 ARG 5 0.12 0.2119 + + 75 CG ARG 5 0.17 81 NE ARG 5 0.155 0.2454 + + 76 HG1 ARG 5 0.12 77 HG2 ARG 5 0.12 0.1745 + + 77 HG2 ARG 5 0.12 78 CD ARG 5 0.17 0.2156 + + 78 CD ARG 5 0.17 79 HD1 ARG 5 0.12 0.1082 + + 78 CD ARG 5 0.17 80 HD2 ARG 5 0.12 0.1091 + + 78 CD ARG 5 0.17 82 HE ARG 5 0.12 0.2079 + + 78 CD ARG 5 0.17 83 CZ ARG 5 0.17 0.2528 + + 79 HD1 ARG 5 0.12 80 HD2 ARG 5 0.12 0.177 + + 79 HD1 ARG 5 0.12 81 NE ARG 5 0.155 0.2117 + + 80 + 80 HD2 ARG 5 0.12 81 NE ARG 5 0.155 0.211 + + 81 NE ARG 5 0.155 82 HE ARG 5 0.12 0.1011 + + 81 NE ARG 5 0.155 84 NH1 ARG 5 0.155 0.2347 + + 81 NE ARG 5 0.155 87 NH2 ARG 5 0.155 0.2296 + + 82 HE ARG 5 0.12 83 CZ ARG 5 0.17 0.2053 + + 83 CZ ARG 5 0.17 85 HH11 ARG 5 0.12 0.2047 + + 83 CZ ARG 5 0.17 86 HH12 ARG 5 0.12 0.2067 + + 83 CZ ARG 5 0.17 88 HH21 ARG 5 0.12 0.204 + + 83 CZ ARG 5 0.17 89 HH22 ARG 5 0.12 0.2059 + + 84 NH1 ARG 5 0.155 85 HH11 ARG 5 0.12 0.1019 + + 84 NH1 ARG 5 0.155 86 HH12 ARG 5 0.12 0.1006 + + 84 NH1 ARG 5 0.155 87 NH2 ARG 5 0.155 0.231 + + 85 HH11 ARG 5 0.12 86 HH12 ARG 5 0.12 0.1717 + + 87 NH2 ARG 5 0.155 88 HH21 ARG 5 0.12 0.1001 + + 87 NH2 ARG 5 0.155 89 HH22 ARG 5 0.12 0.1018 + + 88 HH21 ARG 5 0.12 89 HH22 ARG 5 0.12 0.1722 + + 90 + 90 C ARG 5 0.17 91 O1 ARG 5 0.152 0.125 + + 90 C ARG 5 0.17 92 O2 ARG 5 0.152 0.1236 + + 91 O1 ARG 5 0.152 92 O2 ARG 5 0.152 0.217 + + +no atoms found outside box + + +GROMACS reminds you: "The only greatness for man is immortality." (James Dean) + diff -r 04abdf96978b -r 17c12d5cb336 test-data/check_info_traj.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_info_traj.txt Tue Jul 12 12:44:22 2022 +0000 @@ -0,0 +1,38 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/2/working +Command line: + gmx check -f ./traj.xtc + + +Reading frame 0 time 0.000 +# Atoms 94 +Precision 0.001 (nm) + +Reading frame 1 time 0.100 +Reading frame 2 time 0.200 +Reading frame 3 time 0.300 +Reading frame 4 time 0.400 +Reading frame 5 time 0.500 +Reading frame 6 time 0.600 +Reading frame 7 time 0.700 +Reading frame 8 time 0.800 +Reading frame 9 time 0.900 +Reading frame 10 time 1.000 +Last frame 10 time 1.000 + + +Item #frames Timestep (ps) +Step 11 0.1 +Time 11 0.1 +Lambda 0 +Coords 11 0.1 +Velocities 0 +Forces 0 +Box 11 0.1 + +GROMACS reminds you: "Right Between the Eyes" (F. Zappa) + +Checking file ./traj.xtc diff -r 04abdf96978b -r 17c12d5cb336 test-data/npt2.tpr Binary file test-data/npt2.tpr has changed