view test-data/check_compare_energy.txt @ 4:018628703771 draft default tip

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
author chemteam
date Tue, 12 Jul 2022 12:46:17 +0000
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                 :-) 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