Code: Select all
[06:17:55] Completed 70000 out of 250000 steps (28%)
[06:22:03] Completed 72500 out of 250000 steps (29%)
[06:26:09] Completed 75000 out of 250000 steps (30%)
[06:30:18] Completed 77500 out of 250000 steps (31%)
[06:34:25] Completed 80000 out of 250000 steps (32%)
Step 38831248, time 77662.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000565, max 0.026379 (between atoms 12391 and 12394)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12391 12394 90.0 0.1015 0.1037 0.1010
Step 38831249, time 77662.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000431, max 0.016740 (between atoms 12391 and 12392)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 38831250, time 77662.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000871, max 0.040307 (between atoms 12391 and 12392)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12391 12394 90.0 0.1004 0.1016 0.1010
Step 38831255, time 77662.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001170, max 0.052434 (between atoms 12391 and 12394)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 38831272, time 77662.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001651, max 0.080614 (between atoms 12391 and 12392)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12391 12392 90.0 0.1015 0.1091 0.1010
Step 38831277, time 77662.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001586, max 0.076400 (between atoms 12391 and 12393)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 38831280, time 77662.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001913, max 0.093317 (between atoms 12391 and 12393)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12391 12393 90.0 0.1005 0.1104 0.1010
Step 38831284, time 77662.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001215, max 0.059577 (between atoms 12391 and 12393)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12391 12393 90.0 0.1011 0.1070 0.1010
Step 38831298, time 77662.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.828410, max 37.394680 (between atoms 12391 and 12392)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12388 12389 90.0 0.1089 0.2677 0.1090
12391 12392 90.0 0.1012 3.8779 0.1010
12391 12394 90.0 0.1010 0.2632 0.1010
Warning: 1-4 interaction between 12389 and 12392 at distance 4.018 which is larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 38831299, time 77662.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 197147693879.772186, max 9468738797568.000000 (between atoms 13519 and 13520)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
21608 21609 90.0 0.1090 13359.6699 0.1090
13997 13998 90.0 0.1080 6727528.5000 0.1080
14044 14047 90.0 0.1090 0.5451 0.1090
14122 14124 90.0 0.1010 40820228.0000 0.1010
14064 14065 90.0 0.1010 1.3184 0.1010
13549 13551 90.0 0.1090 0.2031 0.1090
13553 13554 90.0 0.0960 12196.8730 0.0960
14165 14168 90.0 0.1090 10297619.0000 0.1090
14180 14181 95.4 0.1090 266.2557 0.1090
14180 14183 99.2 0.1090 21.0298 0.1090
14184 14185 90.0 0.1090 43254.9336 0.1090
14184 14186 90.1 0.1090 2428.7817 0.1090
21731 21732 90.0 0.0960 9706087.0000 0.0960
12388 12390 90.0 1.8704 0.8861 0.1090
12191 12192 90.0 0.1080 0.6650 0.1080
13450 13452 90.0 0.1090 0.2098 0.1090
13519 13521 90.0 0.1090 4983352832.0000 0.1090
12391 12392 90.0 3.8779 134604881920.0000 0.1010
12391 12393 90.0 0.1097 62355562496.0000 0.1010
12391 12394 90.0 0.2632 13636805632.0000 0.1010
13514 13515 90.0 0.1090 93041.7188 0.1090
13494 13496 90.0 0.1090 10701.5234 0.1090
13446 13447 146.1 0.1090 8.5040 0.1090
13446 13448 90.0 0.1090 188.4226 0.1090
13446 13449 99.3 0.1090 6.1334 0.1090
t = 77662.602 ps: Water molecule starting at atom 123169 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 77662.602 ps: Water molecule starting at atom 36733 can not be settled.
Check for bad contacts and/or reduce the timestep.
Step 38831300:
The charge group starting at atom 21608 moved than the distance allowed by the domain decomposition (1.200000) in direction Z
distance out of cell 38.850372
Old coordinates: 2.677 2.574 5.070
New coordinates: 125.286 124.081 44.822
Old cell boundaries in direction Z: 0.000 6.109
New cell boundaries in direction Z: 0.000 5.971
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: domdec.c, line: 3794
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Step 38831300:
The charge group starting at atom 72634 moved than the distance allowed by the domain decomposition (1.200000) in direction Z
distance out of cell 65.356789
Old coordinates: 3.614 3.981 4.957
New coordinates: 42.559 13.310 72.026
Old cell boundaries in direction Z: 0.000 6.747
New cell boundaries in direction Z: 0.000 6.669
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: domdec.c, line: 3794
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 2, will try to stop all the nodes
Halting parallel program mdrun on CPU 2 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_2]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
[cli_3]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_6]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_1]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_4]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[10:38:11] ***** Got an Activate signal (2)
[10:38:11] Killing all core threads