Mercurial > repos > chemteam > gmx_setup
diff test-data/check_compare_energy.txt @ 21:ea2287ee360b draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
| author | chemteam |
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| date | Tue, 12 Jul 2022 12:46:53 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_compare_energy.txt Tue Jul 12 12:46:53 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