Dear AMBER users,
I have a problem with my minimisation output, as u can see from the output
below, ,from 250 step, the EEL value started to oscillate bewteen about
(-2)*(10^6) to (-8)*(10^7) and then too big to fit the space, and the job
stopped with the error message as 'MPI process rank, caught a SIGSEGV'. As
can be seen, the problematic atom is atom 12159 which named HH (i made it
up), it is a hydrogen atom in a hydrogen molecule that i added in my system.
Can anyone suggest me what shall I do to solve the problem?
Thanks very much in advance!
Rachel
The following is the output:
-----------------------------------------------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.8130E+05 8.6589E+00 1.2311E+03 DH 12158
BOND = 12319.3157 ANGLE = 4262.2942 DIHED =
6788.2453
VDWAALS = 20966.0238 EEL = -264399.8765 HBOND =
0.0000
1-4 VDW = 3817.5022 1-4 EEL = 34943.0628 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -1.8625E+05 2.8188E+00 4.3913E+02 FE 12110
BOND = 11794.4274 ANGLE = 3181.7918 DIHED =
6832.5737
VDWAALS = 18284.3228 EEL = -264556.0346 HBOND =
0.0000
1-4 VDW = 3581.8939 1-4 EEL = 34629.6021 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -1.8731E+05 1.4581E+00 8.3876E+01 FE 12110
BOND = 11728.4379 ANGLE = 2852.5435 DIHED =
6858.0073
VDWAALS = 17976.7772 EEL = -264680.1459 HBOND =
0.0000
1-4 VDW = 3457.5692 1-4 EEL = 34495.5597 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
150 -1.8797E+05 1.2138E+00 9.3236E+01 FE 12110
BOND = 11714.1093 ANGLE = 2680.6319 DIHED =
6875.7728
VDWAALS = 17802.4798 EEL = -264805.0722 HBOND =
0.0000
1-4 VDW = 3365.2133 1-4 EEL = 34401.7260 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -1.8844E+05 1.4438E+00 2.2334E+02 FE 12110
BOND = 11713.6752 ANGLE = 2577.4489 DIHED =
6887.9989
VDWAALS = 17693.9506 EEL = -264938.4370 HBOND =
0.0000
1-4 VDW = 3294.3797 1-4 EEL = 34332.7427 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
250 -1.4001E+07 2.2874E+10 5.3567E+12 CB 1710
BOND = 11724.6116 ANGLE = 2552.7526 DIHED =
6892.6022
VDWAALS = 17660.7588 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4454 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
350 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.4475 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
450 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4465 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.4796 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
550 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4483 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
650 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.5746 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
700 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
750 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4500 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
800 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.5853 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
850 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
900 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4488 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
950 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.6284 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1050 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4489 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1100 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.6596 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1150 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1200 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4602 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1250 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.8262 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1300 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1350 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4600 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1400 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.7398 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1450 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1500 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4562 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1550 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.7172 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1600 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1650 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4629 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1700 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.8409 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1750 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1800 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4659 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1850 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.9068 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1900 -2.1791E+07 5.5955E+10 1.3104E+13 HH 12159
BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = ************* HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1950 -1.9550E+06 3.7414E+08 8.7616E+10 HH 12159
BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
6892.6022
VDWAALS = 17660.7584 EEL = -2031379.4671 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 -8.4332E+06 8.1505E+09 1.9087E+12 HH 12159
BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
6892.6022
VDWAALS = 17660.7587 EEL = -8509648.9202 HBOND =
0.0000
1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
0.0000
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Received on Sun Nov 05 2006 - 06:07:09 PST
