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Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d |
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added:
test-data/check_compare_energy.txt test-data/check_compare_topology.txt test-data/check_compare_traj.txt test-data/check_info_energy.txt test-data/check_info_index.txt test-data/check_info_structure.txt test-data/check_info_traj.txt test-data/npt2.tpr |
| b |
| diff -r 42dfec375136 -r 1f98845f4df4 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 12:51:18 2022 +0000 |
| [ |
| b'@@ -0,0 +1,199 @@\n+ :-) GROMACS - gmx check, 2022-conda_forge (-:\n+\n+Executable: /usr/local/bin.AVX2_256/gmx\n+Data prefix: /usr/local\n+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working\n+Command line:\n+ gmx check -e ./ener1.edr -e2 ./ener2.edr -tol 0.1 -abstol 0.1 -lastener Pressure\n+\n+Opened ./ener1.edr as single precision energy file\n+Opened ./ener2.edr as single precision energy file\n+\n+Reading energy frame 0 time 0.000 \n+Reading energy frame 0 time 0.000 \n+Reading energy frame 1 time 1.000 \n+Reading energy frame 1 time 0.100 \n+Reading energy frame 2 time 2.000 \n+Reading energy frame 2 time 0.200 \n+Reading energy frame 3 time 3.000 \n+Reading energy frame 3 time 0.300 \n+Reading energy frame 4 time 4.000 \n+Reading energy frame 4 time 0.400 comparing energy file ./ener1.edr and ./ener2.edr\n+\n+There are 31 and 50 terms in the energy files\n+\n+enm[0] (Bond - -)\n+enm[30] (T-rest - -)\n+enm[6] (- - Disper. corr.)\n+enm[10] (- - Kinetic En.)\n+enm[11] (- - Total Energy)\n+enm[12] (- - Conserved En.)\n+enm[13] (- - Temperature)\n+enm[14] (- - Pres. DC)\n+enm[16] (- - Constr. rmsd)\n+enm[17] (- - Box-X)\n+enm[18] (- - Box-Y)\n+enm[19] (- - Box-Z)\n+enm[20] (- - Volume)\n+enm[21] (- - Density)\n+enm[22] (- - pV)\n+enm[23] (- - Enthalpy)\n+enm[43] (- - Box-Vel-XX)\n+enm[44] (- - Box-Vel-YY)\n+enm[45] (- - Box-Vel-ZZ)\n+enm[46] (- - T-Protein)\n+enm[47] (- - T-non-Protein)\n+enm[48] (- - Lamb-Protein)\n+enm[49] (- - Lamb-non-Protein)\n+There are 11 terms to compare in the energy files\n+\n+Angle step 0: 659.741, step 0: 174.95\n+Proper Dih. step 0: 93.8665, step 0: 8.40722\n+Ryckaert-Bell. step 0: 69.404, step 0: 91.4765\n+Coulomb-14 step 0: 52.8221, step 0: 135.375\n+LJ (SR) step 0: -13.3421, step 0: -8.41078\n+Coulomb (SR) step 0: -1790.86, step 0: -2038.4\n+Coul. recip. step 0: 959.265, step 0: 615.944\n+Potential step 0: 618.021, step 0: -875.856\n+Pressure step 0: 901.187, step 0: 149.004\n+Vir-XX step 0: -2075.14, step 0: -98.9118\n+t (1.000000e+00 - 1.000000e-01)\n+step (1 - 50)\n+Angle step 1: 536.268, step 1: 188.647\n+Proper Dih. step 1: 88.2, step 1: 17.982\n+Ryckaert-Bell. step 1: 67.8373, step 1: 95.8567\n+Coulomb-14 step 1: 49.6531, step 1: 108.883\n+LJ (SR) step 1: -11.6246, step 1: 9.77759\n+Coulomb (SR) step 1: -1784.23, step 1: -2034.55\n+Coul. recip. step 1: 951.94, step 1: 546.933\n+Potential step 1: 230.009, step 1: -937.817\n+Pressure step 1: 893.094, step 1: 60.2446\n+Vir-XX step 1: -1778.72, step 1: 128.956\n+t (2.000000e+00 - 2.000000e-01)\n+step (2 - 100)\n+Angle step 2: 424.105, step 2: 176.128\n+Proper Dih. step 2: 81.0497, step 2: 13.4277\n+Ryckaert-Bell. step 2: 66.1758, step 2: 112.768\n+Coulomb-14 step 2: 47.7305, step 2: 126.537\n+LJ (SR) step 2: -0.367874, step 2: -9.48936\n+Coulomb (SR) step 2: -1780.95, step 2: -2085.56\n+Coul. recip. step 2: 946.125, step 2: 455.54\n+Potential step 2: -14.5562, step 2: -1076.08\n+Pressure step 2: 675.983, step 2: -57.99\n+Vir-XX step 2: -1371.69, step 2: 247.454\n+t (3.000000e+00 - 3.000000e-01)\n+step (3 - 150)\n+Angle step 3: 237.376, step 3: 205.981\n+Proper Dih. step 3: 68.1909, step 3: 18.2245\n+Ryckaert-Bell. step 3: '..b'3.967\n+t (7.000000e+00 - 6.000000e-01)\n+step (7 - 300)\n+Angle step 7: 130.86, step 7: 193.185\n+Proper Dih. step 7: 42.6816, step 7: 7.0615\n+Ryckaert-Bell. step 7: 53.3748, step 7: 106.945\n+Coulomb-14 step 7: 49.9217, step 7: 100.896\n+LJ (SR) step 7: -15.5538, step 7: 10.2121\n+Coulomb (SR) step 7: -1764.3, step 7: -2143.78\n+Coul. recip. step 7: 924.347, step 7: 311.339\n+Potential step 7: -444.809, step 7: -1304.87\n+Pressure step 7: 215.786, step 7: -61.3894\n+Vir-XX step 7: -589.888, step 7: 192.034\n+t (8.000000e+00 - 7.000000e-01)\n+step (8 - 350)\n+Angle step 8: 68.783, step 8: 187.181\n+Proper Dih. step 8: 30.5271, step 8: 10.9997\n+Ryckaert-Bell. step 8: 49.841, step 8: 123.72\n+Coulomb-14 step 8: 51.1761, step 8: 123.582\n+LJ (SR) step 8: -24.7767, step 8: 48.0457\n+Coulomb (SR) step 8: -1761.91, step 8: -2227.32\n+Coul. recip. step 8: 918.219, step 8: 267.376\n+Potential step 8: -447.838, step 8: -1356\n+Pressure step 8: 255.303, step 8: -36.2835\n+Vir-XX step 8: -410.784, step 8: 5.87002\n+t (1.000000e+01 - 8.000000e-01)\n+step (10 - 400)\n+Angle step 10: 90.876, step 10: 150.124\n+Proper Dih. step 10: 26.773, step 10: 15.4228\n+Ryckaert-Bell. step 10: 49.7648, step 10: 116.734\n+Coulomb-14 step 10: 52.0739, step 10: 120.921\n+LJ (SR) step 10: -24.2058, step 10: 61.3815\n+Coulomb (SR) step 10: -1762.32, step 10: -2208.19\n+Coul. recip. step 10: 918.133, step 10: 281.327\n+Potential step 10: -522.879, step 10: -1339\n+Pressure step 10: 177.827, step 10: 95.8529\n+Vir-XX step 10: -466.151, step 10: 18.0131\n+t (1.200000e+01 - 9.000000e-01)\n+step (12 - 450)\n+Angle step 12: 71.9619, step 12: 218.415\n+Proper Dih. step 12: 20.7858, step 12: 6.46661\n+Ryckaert-Bell. step 12: 48.0374, step 12: 118.772\n+LJ-14 step 12: 113.003, step 12: 125.421\n+Coulomb-14 step 12: 53.485, step 12: 111.128\n+LJ (SR) step 12: -27.637, step 12: 39.4093\n+Coulomb (SR) step 12: -1762.36, step 12: -2201.92\n+Coul. recip. step 12: 915.934, step 12: 272.022\n+Potential step 12: -542.18, step 12: -1310.71\n+Pressure step 12: 180.996, step 12: -77.3705\n+Vir-XX step 12: -403.068, step 12: -3.89205\n+t (1.400000e+01 - 1.000000e+00)\n+step (14 - 500)\n+Angle step 14: 77.708, step 14: 188.913\n+Proper Dih. step 14: 16.917, step 14: 13.1638\n+Ryckaert-Bell. step 14: 47.5084, step 14: 116.045\n+LJ-14 step 14: 112.831, step 14: 128.155\n+Coulomb-14 step 14: 54.3835, step 14: 112.113\n+LJ (SR) step 14: -29.3721, step 14: 18.6406\n+Coulomb (SR) step 1\n+Reading energy frame 11 time 15.000 \n+Last energy frame read 10 time 1.000 \n+GROMACS reminds you: "I do not believe continuum electrostatics" (Arieh Warshel, Nobel lecture 2013)\n+\n+4: -1762.94, step 14: -2187.48\n+Coul. recip. step 14: 914.559, step 14: 304.201\n+Potential step 14: -557.441, step 14: -1306.67\n+Pressure step 14: 144.996, step 14: -10.3104\n+Vir-XX step 14: -396.739, step 14: 362.156\n+\n+End of file on ./ener2.edr but not on ./ener1.edr\n' |
| b |
| diff -r 42dfec375136 -r 1f98845f4df4 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 12:51:18 2022 +0000 |
| [ |
| b'@@ -0,0 +1,287 @@\n+ :-) GROMACS - gmx check, 2022-conda_forge (-:\n+\n+Executable: /usr/local/bin.AVX2_256/gmx\n+Data prefix: /usr/local\n+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working\n+Command line:\n+ gmx check -s1 ./top1.tpr -s2 ./top2.tpr -abstol 0.1\n+\n+Note: When comparing run input files, default tolerances are reduced.\n+Reading file ./top1.tpr, VERSION 2019.1 (single precision)\n+Note: file tpx version 116, software tpx version 127\n+Reading file ./top2.tpr, VERSION 2022-conda_forge (single precision)\n+comparing inputrec\n+inputrec->bContinuation (0 - 1)\n+inputrec->epc (No - Parrinello-Rahman)\n+inputrec->tau_p (1.000000e+00 - 2.000000e+00)\n+inputrec->ref_p(x) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 1.00000e+00 0.00000e+00 0.00000e+00)\n+inputrec->ref_p(y) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 1.00000e+00 0.00000e+00)\n+inputrec->ref_p(z) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 0.00000e+00 1.00000e+00)\n+refcoord_scaling (COM - No)\n+inputrec->posres_com ( 4.98028e-01 4.93806e-01 5.09595e-01) - ( 0.00000e+00 0.00000e+00 0.00000e+00)\n+inputrec->posres_comB ( 4.98028e-01 4.93806e-01 5.09595e-01) - ( 0.00000e+00 0.00000e+00 0.00000e+00)\n+inputrec->ld_seed (-1065163585 - -1245840145)\n+comparing mtop topology\n+comparing force field parameters\n+numTypes (238 - 195)\n+ffparams->functype[181][181] (52 - 62)\n+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)\n+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)\n+ffparams->functype[182][182] (52 - 62)\n+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)\n+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)\n+ffparams->functype[183][183] (52 - 62)\n+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)\n+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)\n+ffparams->functype[184][184] (52 - 62)\n+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)\n+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)\n+ffparams->functype[185][185] (52 - 62)\n+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)\n+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, 0.00000000'..b'- ( 2.19200e+00 2.52400e+00 2.13400e+00)\n+x[ 53] ( 2.19300e+00 2.61000e+00 2.08100e+00) - ( 2.17400e+00 2.62100e+00 2.09100e+00)\n+x[ 54] ( 2.33200e+00 2.37400e+00 2.26900e+00) - ( 2.30700e+00 2.38200e+00 2.29600e+00)\n+x[ 55] ( 2.41100e+00 2.35700e+00 2.32800e+00) - ( 2.37800e+00 2.36900e+00 2.37600e+00)\n+x[ 56] ( 2.30900e+00 2.50200e+00 2.21800e+00) - ( 2.28200e+00 2.50800e+00 2.24000e+00)\n+x[ 57] ( 2.36700e+00 2.57900e+00 2.24600e+00) - ( 2.33500e+00 2.59400e+00 2.27800e+00)\n+x[ 58] ( 2.01900e+00 1.95900e+00 2.00800e+00) - ( 2.03500e+00 1.96000e+00 2.01800e+00)\n+x[ 59] ( 1.89700e+00 1.93100e+00 1.99900e+00) - ( 1.93600e+00 1.90800e+00 1.96700e+00)\n+x[ 60] ( 2.11700e+00 1.87900e+00 2.05200e+00) - ( 2.11600e+00 1.89700e+00 2.10300e+00)\n+x[ 61] ( 2.21200e+00 1.91000e+00 2.05300e+00) - ( 2.17200e+00 1.95000e+00 2.16800e+00)\n+x[ 62] ( 2.08200e+00 1.74300e+00 2.09800e+00) - ( 2.08300e+00 1.76000e+00 2.13800e+00)\n+x[ 63] ( 2.00700e+00 1.70700e+00 2.04200e+00) - ( 2.01900e+00 1.70400e+00 2.06900e+00)\n+x[ 64] ( 2.16100e+00 1.68300e+00 2.09100e+00) - ( 2.17700e+00 1.71100e+00 2.16100e+00)\n+x[ 65] ( 2.03700e+00 1.75700e+00 2.24300e+00) - ( 2.00800e+00 1.78300e+00 2.26900e+00)\n+x[ 66] ( 2.07500e+00 1.85500e+00 2.30700e+00) - ( 1.98300e+00 1.89000e+00 2.32300e+00)\n+x[ 67] ( 1.95000e+00 1.66900e+00 2.28800e+00) - ( 1.96400e+00 1.67400e+00 2.33300e+00)\n+x[ 68] ( 1.91600e+00 1.59900e+00 2.22500e+00) - ( 2.00100e+00 1.58400e+00 2.30700e+00)\n+x[ 69] ( 1.90100e+00 1.66900e+00 2.42600e+00) - ( 1.90200e+00 1.66500e+00 2.46400e+00)\n+x[ 70] ( 1.84300e+00 1.74900e+00 2.43300e+00) - ( 1.85200e+00 1.75700e+00 2.49300e+00)\n+x[ 71] ( 1.82100e+00 1.54100e+00 2.45200e+00) - ( 1.79000e+00 1.56300e+00 2.44200e+00)\n+x[ 72] ( 1.74500e+00 1.53700e+00 2.38800e+00) - ( 1.76700e+00 1.56100e+00 2.33500e+00)\n+x[ 73] ( 1.88100e+00 1.46200e+00 2.43800e+00) - ( 1.82100e+00 1.46000e+00 2.45400e+00)\n+x[ 74] ( 1.76600e+00 1.53500e+00 2.59300e+00) - ( 1.68200e+00 1.57700e+00 2.54900e+00)\n+x[ 75] ( 1.84200e+00 1.53200e+00 2.65800e+00) - ( 1.65100e+00 1.68000e+00 2.56200e+00)\n+x[ 76] ( 1.71000e+00 1.61600e+00 2.61000e+00) - ( 1.58800e+00 1.54200e+00 2.50700e+00)\n+x[ 77] ( 1.68300e+00 1.41500e+00 2.61300e+00) - ( 1.70700e+00 1.49400e+00 2.67500e+00)\n+x[ 78] ( 1.64900e+00 1.41400e+00 2.70700e+00) - ( 1.77900e+00 1.52800e+00 2.75000e+00)\n+x[ 79] ( 1.60500e+00 1.42000e+00 2.55000e+00) - ( 1.61600e+00 1.49900e+00 2.73500e+00)\n+x[ 80] ( 1.75100e+00 1.29000e+00 2.58900e+00) - ( 1.73200e+00 1.35300e+00 2.64800e+00)\n+x[ 81] ( 1.74700e+00 1.25500e+00 2.49600e+00) - ( 1.64100e+00 1.31200e+00 2.63200e+00)\n+x[ 82] ( 1.81800e+00 1.21600e+00 2.67500e+00) - ( 1.83600e+00 1.27300e+00 2.67800e+00)\n+x[ 83] ( 1.82900e+00 1.24800e+00 2.80400e+00) - ( 1.94600e+00 1.33800e+00 2.71700e+00)\n+x[ 84] ( 1.78400e\n+GROMACS reminds you: "Pain is inevitable. Suffering is optional." (Haruki Murakami)\n+\n++00 1.33100e+00 2.83800e+00) - ( 1.94400e+00 1.43900e+00 2.72300e+00)\n+x[ 85] ( 1.88100e+00 1.19000e+00 2.86600e+00) - ( 2.03900e+00 1.29700e+00 2.71100e+00)\n+x[ 86] ( 1.87000e+00 1.09900e+00 2.63200e+00) - ( 1.83400e+00 1.14000e+00 2.66600e+00)\n+x[ 87] ( 1.85600e+00 1.07000e+00 2.53800e+00) - ( 1.75700e+00 1.09400e+00 2.62000e+00)\n+x[ 88] ( 1.92100e+00 1.04100e+00 2.69500e+00) - ( 1.90200e+00 1.08100e+00 2.71200e+00)\n+x[ 89] ( 2.01200e+00 1.68800e+00 2.52900e+00) - ( 2.00200e+00 1.59300e+00 2.55400e+00)\n+x[ 90] ( 2.01200e+00 1.78000e+00 2.61500e+00) - ( 1.96600e+00 1.60300e+00 2.67300e+00)\n+x[ 91] ( 1.97500e+00 1.68900e+00 2.66000e+00) - ( 2.09800e+00 1.52500e+00 2.51200e+00)\n+x[ 92] ( 8.65000e-01 2.21000e+00 2.05700e+00) - ( 1.57100e+00 2.29900e+00 1.78700e+00)\n+x[ 93] ( 2.87900e+00 3.76300e+00 2.61500e+00) - ( 2.64400e+00 3.40800e+00 2.32600e+00)\n+comparing v\n' |
| b |
| diff -r 42dfec375136 -r 1f98845f4df4 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 12:51:18 2022 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 42dfec375136 -r 1f98845f4df4 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 12:51:18 2022 +0000 |
| b |
| @@ -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) + |
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| diff -r 42dfec375136 -r 1f98845f4df4 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 12:51:18 2022 +0000 |
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| @@ -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 |
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| diff -r 42dfec375136 -r 1f98845f4df4 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 12:51:18 2022 +0000 |
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| b'@@ -0,0 +1,480 @@\n+ :-) GROMACS - gmx check, 2022-conda_forge (-:\n+\n+Executable: /usr/local/bin.AVX2_256/gmx\n+Data prefix: /usr/local\n+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working\n+Command line:\n+ gmx check -c ./struc.gro -vdwfac 0.8 -bonlo 0.4 -bonhi 0.7\n+\n+Checking coordinate file ./struc.gro\n+94 atoms in file\n+coordinates found\n+box found\n+velocities absent\n+\n+Checking for atoms closer than 0.8 and not between 0.4 and 0.7,\n+relative to sum of Van der Waals distance:\n+\n+WARNING: Masses and atomic (Van der Waals) radii will be guessed\n+ based on residue and atom names, since they could not be\n+ definitively assigned from the information in your input\n+ files. These guessed numbers might deviate from the mass\n+ and radius of the atom type. Please check the output\n+ files if necessary. Note, that this functionality may\n+ be removed in a future GROMACS version. Please, consider\n+ using another file format for your input.\n+\n+\n+WARNING: Masses and atomic (Van der Waals) radii will be guessed\n+ based on residue and atom names, since they could not be\n+ definitively assigned from the information in your input\n+ files. These guessed numbers might deviate from the mass\n+ and radius of the atom type. Please check the output\n+ files if necessary. Note, that this functionality may\n+ be removed in a future GROMACS version. Please, consider\n+ using another file format for your input.\n+\n+NOTE: From version 5.0 gmx check uses the Van der Waals radii\n+from the source below. This means the results may be different\n+compared to previous GROMACS versions.\n+\n+++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n+A. Bondi\n+van der Waals Volumes and Radii\n+J. Phys. Chem. 68 (1964) pp. 441-451\n+-------- -------- --- Thank You --- -------- --------\n+\n+\n+atom# name residue r_vdw atom# name residue r_vdw distance\n+\n+ 1 N LYS 1 0.155 2 H1 LYS 1 0.12 0.1008\n+\n+ 1 N LYS 1 0.155 3 H2 LYS 1 0.12 0.1012\n+\n+ 1 N LYS 1 0.155 4 H3 LYS 1 0.12 0.1019\n+\n+ 1 N LYS 1 0.155 6 HA LYS 1 0.12 0.2103\n+\n+ 1 N LYS 1 0.155 7 CB LYS 1 0.17 0.2447\n+\n+ 1 N LYS 1 0.155 23 C LYS 1 0.17 0.2437\n+\n+ 2 H1 LYS 1 0.12 5 CA LYS 1 0.17 0.205 \n+\n+ 3 H2 LYS 1 0.12 5 CA LYS 1 0.17 0.204 \n+\n+ 5 CA LYS 1 0.17 6 HA LYS 1 0.12 0.1093\n+\n+ 5 CA LYS 1 0.17 8 HB1 LYS 1 0.12 0.2166\n+\n+ 5 CA LYS 1 0.17 9 HB2 LYS 1 0.12 0.2169\n+\n+ 5 CA LYS 1 0.17 10 CG LYS 1 0.17 0.2598\n+\n+ 5 CA LYS 1 0.17 24 O LYS 1 0.152 0.235 \n+\n+ 5 CA LYS 1 0.17 25 N VAL 2 0.155 0.2455\n+\n+ 6 HA LYS 1 0.12 7 CB LYS 1 0.17 0.2176\n+\n+ 6 HA LYS 1 0.12 23 C LYS 1 0.17 0.215 \n+\n+ 7 CB LYS 1 0.17 8 HB1 LYS 1 0.12 0.1093\n+\n+ 7 CB LYS 1 0.17 9 HB2 LYS 1 0.12 0.1089\n+\n+ 7 CB LYS 1 0.17 11 HG1 LYS 1 0.12 0.2154\n+\n+ 7 CB LYS 1 0.17 12 HG2 LYS 1 0.12 0.217 \n+\n+ 7 CB LYS 1 0.17 13 CD LYS 1 0.17 0.252 \n+\n+ 7 CB LYS 1 0.17 23 C LYS 1 0.17 0.2504\n+\n+ 8 HB1 LYS 1 0.12 9 HB2 LYS 1 0.12 0.1744\n+\n+ 8 HB1 LYS 1 0.12 10 CG LYS 1 0.17 0.2149\n+\n+ 9 HB2 LYS 1 0.12 10 CG LYS 1 0.17 0.2132\n+\n+ 10\n+ 10 CG LYS 1 0.17 11 HG1 LYS 1 0.12 0.1093\n+\n+ 10 CG LYS 1 0.17 12 HG2 LYS 1 0.12 0.1094\n+\n+ 10 CG LYS 1 0.17 14 HD1 LYS 1 0.12 0.2135\n+\n+ 10 CG LYS 1 0.17 15 HD2 LYS 1 0.12 0.2152\n+\n+ 10 CG LYS 1 0.17 16 CE LYS 1 0.17 0.251 \n+\n+ 11 HG1 LYS 1 0.12 12 HG2 LYS 1 0.12 0.1752\n+\n+ 11 HG1 LYS '..b'0.152 0.2357\n+\n+ 63 CA GLY 4 0.17 68 N ARG 5 0.155 0.2453\n+\n+ 64 HA1 GLY 4 0.12 65 HA2 GLY 4 0.12 0.1769\n+\n+ 64 HA1 GLY 4 0.12 66 C GLY 4 0.17 0.2199\n+\n+ 65 HA2 GLY 4 0.12 66 C GLY 4 0.17 0.214 \n+\n+ 66 C GLY 4 0.17 67 O GLY 4 0.152 0.1224\n+\n+ 66 C GLY 4 0.17 70 CA ARG 5 0.17 0.2528\n+\n+ 67 O GLY 4 0.152 68 N ARG 5 0.155 0.2269\n+\n+ 68 N ARG 5 0.155 69 H ARG 5 0.12 0.1006\n+\n+ 68 N ARG 5 0.155 71 HA ARG 5 0.12 0.2006\n+\n+ 68 N ARG 5 0.155 72 CB ARG 5 0.17 0.2455\n+\n+ 69 H ARG 5 0.12 70 CA ARG 5 0.17 0.2121\n+\n+ 70\n+ 70 CA ARG 5 0.17 71 HA ARG 5 0.12 0.1085\n+\n+ 70 CA ARG 5 0.17 73 HB1 ARG 5 0.12 0.217 \n+\n+ 70 CA ARG 5 0.17 74 HB2 ARG 5 0.12 0.2158\n+\n+ 70 CA ARG 5 0.17 75 CG ARG 5 0.17 0.2571\n+\n+ 70 CA ARG 5 0.17 91 O1 ARG 5 0.152 0.2432\n+\n+ 70 CA ARG 5 0.17 92 O2 ARG 5 0.152 0.2442\n+\n+ 71 HA ARG 5 0.12 72 CB ARG 5 0.17 0.2124\n+\n+ 71 HA ARG 5 0.12 90 C ARG 5 0.17 0.2062\n+\n+ 72 CB ARG 5 0.17 73 HB1 ARG 5 0.12 0.1104\n+\n+ 72 CB ARG 5 0.17 74 HB2 ARG 5 0.12 0.1091\n+\n+ 72 CB ARG 5 0.17 76 HG1 ARG 5 0.12 0.2188\n+\n+ 72 CB ARG 5 0.17 77 HG2 ARG 5 0.12 0.2156\n+\n+ 72 CB ARG 5 0.17 78 CD ARG 5 0.17 0.2564\n+\n+ 72 CB ARG 5 0.17 90 C ARG 5 0.17 0.2656\n+\n+ 73 HB1 ARG 5 0.12 74 HB2 ARG 5 0.12 0.1759\n+\n+ 73 HB1 ARG 5 0.12 75 CG ARG 5 0.17 0.2148\n+\n+ 74 HB2 ARG 5 0.12 75 CG ARG 5 0.17 0.217 \n+\n+ 75 CG ARG 5 0.17 76 HG1 ARG 5 0.12 0.1079\n+\n+ 75 CG ARG 5 0.17 77 HG2 ARG 5 0.12 0.1091\n+\n+ 75 CG ARG 5 0.17 79 HD1 ARG 5 0.12 0.2096\n+\n+ 75 CG ARG 5 0.17 80 HD2 ARG 5 0.12 0.2119\n+\n+ 75 CG ARG 5 0.17 81 NE ARG 5 0.155 0.2454\n+\n+ 76 HG1 ARG 5 0.12 77 HG2 ARG 5 0.12 0.1745\n+\n+ 77 HG2 ARG 5 0.12 78 CD ARG 5 0.17 0.2156\n+\n+ 78 CD ARG 5 0.17 79 HD1 ARG 5 0.12 0.1082\n+\n+ 78 CD ARG 5 0.17 80 HD2 ARG 5 0.12 0.1091\n+\n+ 78 CD ARG 5 0.17 82 HE ARG 5 0.12 0.2079\n+\n+ 78 CD ARG 5 0.17 83 CZ ARG 5 0.17 0.2528\n+\n+ 79 HD1 ARG 5 0.12 80 HD2 ARG 5 0.12 0.177 \n+\n+ 79 HD1 ARG 5 0.12 81 NE ARG 5 0.155 0.2117\n+\n+ 80\n+ 80 HD2 ARG 5 0.12 81 NE ARG 5 0.155 0.211 \n+\n+ 81 NE ARG 5 0.155 82 HE ARG 5 0.12 0.1011\n+\n+ 81 NE ARG 5 0.155 84 NH1 ARG 5 0.155 0.2347\n+\n+ 81 NE ARG 5 0.155 87 NH2 ARG 5 0.155 0.2296\n+\n+ 82 HE ARG 5 0.12 83 CZ ARG 5 0.17 0.2053\n+\n+ 83 CZ ARG 5 0.17 85 HH11 ARG 5 0.12 0.2047\n+\n+ 83 CZ ARG 5 0.17 86 HH12 ARG 5 0.12 0.2067\n+\n+ 83 CZ ARG 5 0.17 88 HH21 ARG 5 0.12 0.204 \n+\n+ 83 CZ ARG 5 0.17 89 HH22 ARG 5 0.12 0.2059\n+\n+ 84 NH1 ARG 5 0.155 85 HH11 ARG 5 0.12 0.1019\n+\n+ 84 NH1 ARG 5 0.155 86 HH12 ARG 5 0.12 0.1006\n+\n+ 84 NH1 ARG 5 0.155 87 NH2 ARG 5 0.155 0.231 \n+\n+ 85 HH11 ARG 5 0.12 86 HH12 ARG 5 0.12 0.1717\n+\n+ 87 NH2 ARG 5 0.155 88 HH21 ARG 5 0.12 0.1001\n+\n+ 87 NH2 ARG 5 0.155 89 HH22 ARG 5 0.12 0.1018\n+\n+ 88 HH21 ARG 5 0.12 89 HH22 ARG 5 0.12 0.1722\n+\n+ 90\n+ 90 C ARG 5 0.17 91 O1 ARG 5 0.152 0.125 \n+\n+ 90 C ARG 5 0.17 92 O2 ARG 5 0.152 0.1236\n+\n+ 91 O1 ARG 5 0.152 92 O2 ARG 5 0.152 0.217 \n+\n+ \n+no atoms found outside box\n+\n+\n+GROMACS reminds you: "The only greatness for man is immortality." (James Dean)\n+\n' |
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| diff -r 42dfec375136 -r 1f98845f4df4 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 12:51:18 2022 +0000 |
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| @@ -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 |
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| diff -r 42dfec375136 -r 1f98845f4df4 test-data/npt2.tpr |
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| Binary file test-data/npt2.tpr has changed |