[gmx-users] version 3.3 - Range checking error
Joanne Hanna
J.F.Hanna at warwick.ac.uk
Fri Nov 25 15:19:57 CET 2005
Not knowing how significant differences would have to be to be a porblem. Here is the first 500 steps output (at every 100 steps).
:-) G R O M A C S (-:
GROwing Monsters And Cloning Shrimps
:-) VERSION 3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) gmxcheck_d (double precision) (-:
comparing energy file eners.edr and enerd.edr
There are 72 terms in the energy files
There are 72 terms to compare in the energy files
Pressure (bar) step 0: 432.965, step 0: 434.614
pV step 0: 20071.6, step 0: 20148
Vir-XX step 0: 51368.9, step 0: 51112.8
Vir-XY step 0: 257.462, step 0: 93.3537
Vir-XZ step 0: -1532.22, step 0: -1458.25
Vir-YX step 0: 282.26, step 0: 93.3537
Vir-YY step 0: 52179.4, step 0: 52345.7
Vir-YZ step 0: 1095.51, step 0: 1121.96
Vir-ZX step 0: -1619.66, step 0: -1458.25
Vir-ZY step 0: 1105.87, step 0: 1121.96
Pres-XX (bar) step 0: 490.341, step 0: 501.277
Pres-XY (bar) step 0: 2.17027, step 0: 9.24938
Pres-XZ (bar) step 0: 73.016, step 0: 69.8262
Pres-YX (bar) step 0: 1.10044, step 0: 9.24938
Pres-YY (bar) step 0: 443.967, step 0: 436.673
Pres-YZ (bar) step 0: -49.8571, step 0: -51.0073
Pres-ZX (bar) step 0: 76.7884, step 0: 69.8262
Pres-ZY (bar) step 0: -50.304, step 0: -51.0073
Pres-ZZ (bar) step 0: 364.587, step 0: 365.891
#Surf*SurfTen step 0: -837.452, step 0: -841.679
Pressure (bar) step 100: 333.024, step 100: 325.708
pV step 100: 15438.8, step 100: 15099.6
Vir-XX step 100: 53317.6, step 100: 53483
Vir-XY step 100: -856.207, step 100: -584.384
Vir-XZ step 100: -565.498, step 100: -402.391
Vir-YX step 100: -878.677, step 100: -584.384
Vir-YY step 100: 54712.9, step 100: 54966.4
Vir-YZ step 100: -4465.71, step 100: -4341.7
Vir-ZX step 100: -603.512, step 100: -402.391
Vir-ZY step 100: -4415.76, step 100: -4341.7
Vir-ZZ step 100: 57686.8, step 100: 57767.4
Pres-XX (bar) step 100: 419.622, step 100: 412.412
Pres-XY (bar) step 100: 31.245, step 100: 19.3571
Pres-XZ (bar) step 100: 18.5877, step 100: 11.4648
Pres-YX (bar) step 100: 32.2144, step 100: 19.3571
Pres-YY (bar) step 100: 335.811, step 100: 324.853
Pres-YZ (bar) step 100: 186.415, step 100: 181.05
Pres-ZX (bar) step 100: 20.2276, step 100: 11.4648
Pres-ZY (bar) step 100: 184.26, step 100: 181.05
Pres-ZZ (bar) step 100: 243.638, step 100: 239.859
#Surf*SurfTen step 100: -1094.75, step 100: -1051.44
Box-Vel-XX step 100: 0.00070444, step 100: 0.000703141
Box-Vel-YY step 100: 0.000664152, step 100: 0.000662928
Box-Vel-ZZ step 100: 0.000575173, step 100: 0.000574113
Xi-Protein step 100: -0.0208279, step 100: -0.0208923
Xi-SOLVENT step 100: -0.00397554, step 100: -0.00400168
Pressure (bar) step 200: 364.367, step 200: 354.819
pV step 200: 16893, step 200: 16450.3
Vir-XX step 200: 52529, step 200: 52748.3
Vir-XY step 200: -2632.46, step 200: -2472.15
Vir-XZ step 200: 854.024, step 200: 923.575
Vir-YX step 200: -2741.21, step 200: -2472.15
Vir-YZ step 200: 730.618, step 200: 1194.33
Vir-ZX step 200: 857.574, step 200: 923.575
Vir-ZY step 200: 1000.48, step 200: 1194.33
Vir-ZZ step 200: 59607.2, step 200: 59935.1
Pres-XX (bar) step 200: 489.719, step 200: 476.374
Pres-XY (bar) step 200: 116.015, step 200: 108.287
Pres-XZ (bar) step 200: -51.0944, step 200: -52.4973
Pres-YX (bar) step 200: 120.706, step 200: 108.287
Pres-YY (bar) step 200: 457.028, step 200: 453.289
Pres-YZ (bar) step 200: -21.0133, step 200: -41.917
Pres-ZX (bar) step 200: -51.2476, step 200: -52.4973
Pres-ZY (bar) step 200: -32.6549, step 200: -41.917
Pres-ZZ (bar) step 200: 146.355, step 200: 134.795
#Surf*SurfTen step 200: -2670.17, step 200: -2694.82
Box-Vel-XX step 200: 0.00153721, step 200: 0.00153256
Box-Vel-YY step 200: 0.00144929, step 200: 0.00144492
Box-Vel-ZZ step 200: 0.00125513, step 200: 0.00125133
Mu-X step 200: -763.59, step 200: -753.875
Mu-Y step 200: -1594.79, step 200: -1586.89
Mu-Z step 200: -592.378, step 200: -568.33
Coul-SR:Protein-NA+ step 200: -28.1229, step 200: -28.3109
LJ-SR:Protein-NA+ step 200: -0.871013, step 200: -0.872491
LJ-SR:SOL-NA+ step 200: 784.009, step 200: 785.766
Xi-Protein step 200: -0.0434529, step 200: -0.0435017
Xi-SOLVENT step 200: -0.0113163, step 200: -0.0112383
G96Angle step 300: 8414.08, step 300: 8431.86
Improper Dih. step 300: 2446.87, step 300: 2468.5
LJ-14 step 300: 415.298, step 300: 419.523
LJ (SR) step 300: 139384, step 300: 139752
Kinetic En. step 300: 190412, step 300: 189864
Temperature step 300: 309.301, step 300: 308.411
Pressure (bar) step 300: 467.377, step 300: 517.284
pV step 300: 21671.4, step 300: 23985.5
Vir-XX step 300: 49356.1, step 300: 47295.7
Vir-XY step 300: -409.223, step 300: -498.354
Vir-XZ step 300: 1156.98, step 300: -14.0406
Vir-YX step 300: -798.629, step 300: -498.354
Vir-YY step 300: 56742.4, step 300: 55983.9
Vir-YZ step 300: 483.064, step 300: -837.555
Vir-ZX step 300: 880.388, step 300: -14.0406
Vir-ZY step 300: 725.96, step 300: -837.555
Vir-ZZ step 300: 51805.9, step 300: 50605.9
Pres-XX (bar) step 300: 622.956, step 300: 708.812
Pres-XY (bar) step 300: 9.80198, step 300: 12.4903
Pres-XZ (bar) step 300: -39.9722, step 300: 7.09068
Pres-YX (bar) step 300: 26.5983, step 300: 12.4903
Pres-YY (bar) step 300: 286.663, step 300: 301.268
Pres-YZ (bar) step 300: -35.278, step 300: 21.6577
Pres-ZX (bar) step 300: -28.0421, step 300: 7.09068
Pres-ZY (bar) step 300: -45.7548, step 300: 21.6577
Pres-ZZ (bar) step 300: 492.512, step 300: 541.773
#Surf*SurfTen step 300: 307.861, step 300: 299.944
Box-Vel-XX step 300: 0.00246476, step 300: 0.00246871
Box-Vel-YY step 300: 0.0023238, step 300: 0.00232752
Box-Vel-ZZ step 300: 0.00201247, step 300: 0.00201569
Mu-X step 300: -548.797, step 300: -597.337
Mu-Y step 300: -1855.95, step 300: -1887.16
Mu-Z step 300: -217.058, step 300: -253.537
Coul-SR:Protein-Protein step 300: -19655.9, step 300: -19682.5
LJ-14:Protein-Protein step 300: 415.298, step 300: 419.523
Coul-SR:Protein-SOL step 300: -31465.9, step 300: -31420.5
LJ-SR:Protein-SOL step 300: -3304.97, step 300: -3296.09
Coul-SR:Protein-NA+ step 300: -6.70645, step 300: -8.82074
LJ-SR:Protein-NA+ step 300: -0.87207, step 300: -0.886125
LJ-SR:SOL-SOL step 300: 159792, step 300: 160130
Coul-SR:SOL-NA+ step 300: -6331.76, step 300: -6425.61
LJ-SR:SOL-NA+ step 300: 695.463, step 300: 708.906
T-Protein step 300: 316.357, step 300: 315.259
T-SOLVENT step 300: 308.772, step 300: 307.897
Xi-Protein step 300: -0.0390033, step 300: -0.0397405
Xi-SOLVENT step 300: -0.0135761, step 300: -0.0130915
G96Angle step 400: 8474.17, step 400: 8492.43
Proper Dih. step 400: 3737.39, step 400: 3745.29
Improper Dih. step 400: 2523.96, step 400: 2512.12
LJ-14 step 400: 396.242, step 400: 355.992
LJ (SR) step 400: 140114, step 400: 139338
Pressure (bar) step 400: 529.958, step 400: 483.65
pV step 400: 24577.6, step 400: 22430.1
Vir-XX step 400: 50328.1, step 400: 53709.8
Vir-XY step 400: 694.578, step 400: 737.44
Vir-XZ step 400: -1901, step 400: 2106.76
Vir-YX step 400: 874.627, step 400: 737.44
Vir-YY step 400: 52607.5, step 400: 49280
Vir-YZ step 400: 1763.98, step 400: -2585.38
Vir-ZX step 400: -1431.88, step 400: 2106.76
Vir-ZY step 400: 1976.41, step 400: -2585.38
Vir-ZZ step 400: 51722.2, step 400: 54853.4
Pres-XX (bar) step 400: 570.33, step 400: 437.664
Pres-XY (bar) step 400: -16.6754, step 400: -23.7204
Pres-XZ (bar) step 400: 72.7748, step 400: -95.3356
Pres-YX (bar) step 400: -24.4401, step 400: -23.7204
Pres-YY (bar) step 400: 484.424, step 400: 608.446
Pres-YZ (bar) step 400: -68.7346, step 400: 113.886
Pres-ZX (bar) step 400: 52.5439, step 400: -95.3356
Pres-ZY (bar) step 400: -77.8956, step 400: 113.886
Pres-ZZ (bar) step 400: 535.12, step 400: 404.841
#Surf*SurfTen step 400: 63.2335, step 400: -965.34
Box-Vel-XX step 400: 0.00369803, step 400: 0.00374974
Box-Vel-YY step 400: 0.00348653, step 400: 0.00353529
Box-Vel-ZZ step 400: 0.00301943, step 400: 0.00306166
Mu-X step 400: -870.072, step 400: -988.95
Mu-Y step 400: -1581.75, step 400: -1513.22
Mu-Z step 400: -97.259, step 400: -415.958
Coul-SR:Protein-Protein step 400: -19427.9, step 400: -19326.2
LJ-SR:Protein-Protein step 400: -17825.3, step 400: -17865.3
LJ-14:Protein-Protein step 400: 396.242, step 400: 355.992
LJ-SR:Protein-SOL step 400: -2837.71, step 400: -2860.36
Coul-SR:Protein-NA+ step 400: -19.9423, step 400: -25.1193
LJ-SR:Protein-NA+ step 400: -0.922045, step 400: -0.948589
LJ-SR:SOL-SOL step 400: 160040, step 400: 159279
Coul-SR:SOL-NA+ step 400: -6370.13, step 400: -6412.6
LJ-SR:SOL-NA+ step 400: 737.319, step 400: 785.839
Coul-SR:NA+-NA+ step 400: 0.00201001, step 400: 0.00417869
LJ-SR:NA+-NA+ step 400: -8.00207e-05, step 400: -9.95711e-05
T-Protein step 400: 315.963, step 400: 315.576
Xi-Protein step 400: -0.021856, step 400: -0.0227436
Xi-SOLVENT step 400: -0.0095382, step 400: -0.0121063
G96Angle step 500: 8488.82, step 500: 8509.41
Proper Dih. step 500: 3754.14, step 500: 3666.27
Improper Dih. step 500: 2588.38, step 500: 2697.11
LJ-14 step 500: 431.919, step 500: 520
Coulomb (SR) step 500: -1.05681e+06, step 500: -1.05555e+06
Coul. recip. step 500: -168508, step 500: -168699
Potential step 500: -1.01274e+06, step 500: -1.01152e+06
Kinetic En. step 500: 192211, step 500: 191416
Temperature step 500: 312.225, step 500: 310.933
Pressure (bar) step 500: 456.044, step 500: 465.154
pV step 500: 21155.2, step 500: 21577.9
Vir-XX step 500: 53671.2, step 500: 54244.3
Vir-XY step 500: 1888.16, step 500: 989.344
Vir-XZ step 500: 761.907, step 500: 371.834
Vir-YX step 500: 1683.44, step 500: 989.344
Vir-YY step 500: 51893.6, step 500: 52405.1
Vir-YZ step 500: 1518.35, step 500: 3574.17
Vir-ZX step 500: 718.737, step 500: 371.834
Vir-ZY step 500: 1566.6, step 500: 3574.17
Vir-ZZ step 500: 54913.7, step 500: 52399.8
Pres-XX (bar) step 500: 461.311, step 500: 415.033
Pres-XY (bar) step 500: -90.0561, step 500: -57.6901
Pres-XZ (bar) step 500: -31.1686, step 500: -18.29
Pres-YX (bar) step 500: -81.2298, step 500: -57.6901
Pres-YY (bar) step 500: 517.91, step 500: 480.745
Pres-YZ (bar) step 500: -61.8217, step 500: -159.043
Pres-ZX (bar) step 500: -29.3073, step 500: -18.29
Pres-ZY (bar) step 500: -63.9016, step 500: -159.043
Pres-ZZ (bar) step 500: 388.91, step 500: 499.685
#Surf*SurfTen step 500: -822.393, step 500: 423.004
Box-Vel-XX step 500: 0.00482563, step 500: 0.00495753
Box-Vel-YY step 500: 0.00454964, step 500: 0.00467401
Box-Vel-ZZ step 500: 0.00394011, step 500: 0.00404781
Mu-X step 500: -1112.28, step 500: -788.815
Mu-Y step 500: -1666.1, step 500: -1893.62
Mu-Z step 500: -342.312, step 500: -67.8046
Coul-SR:Protein-Protein step 500: -19330.1, step 500: -19375.6
LJ-SR:Protein-Protein step 500: -17901.3, step 500: -17948.5
LJ-14:Protein-Protein step 500: 431.919, step 500: 520
Coul-SR:Protein-SOL step 500: -31990.9, step 500: -32063.3
LJ-SR:Protein-SOL step 500: -3125.25, step 500: -2939.94
Coul-SR:Protein-NA+ step 500: -5.75253, step 500: -31.4877
LJ-SR:Protein-NA+ step 500: -0.854334, step 500: -0.942451
Coul-SR:SOL-SOL step 500: -999022, step 500: -997781
Coul-SR:SOL-NA+ step 500: -6465.61, step 500: -6303.14
LJ-SR:SOL-NA+ step 500: 794.824, step 500: 737.805
Coul-SR:NA+-NA+ step 500: 0, step 500: 0.00219784
LJ-SR:NA+-NA+ step 500: 0, step 500: -8.2122e-05
T-Protein step 500: 311.463, step 500: 318.827
T-SOLVENT step 500: 312.282, step 500: 310.34
Xi-Protein step 500: 0.0124343, step 500: 0.0197079
Xi-SOLVENT step 500: -0.00366325, step 500: -0.0089186
Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL
J.F.Hanna at warwick.ac.uk
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