[gmx-users] Regarding Production MD error
kirubakaran palani
kirubakaran17 at gmail.com
Sun Aug 19 09:40:58 CEST 2012
Dear Users,
I am running the final MD of my protein ligand complex in 16 processor
node for 30ns in gromacs455 version. There, in 9th ns it stops and
giving error message like given below. What could be the reason for
this and how to rectify this error.
Any help will be highly appreciated.
Urs,
Kirubakaran P
Error msg given below,
==================================================================================================
Step 4500632, time 9001.26 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000105, max 0.002448 (between atoms 3333 and 3332)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3333 3332 30.3 0.1094 0.1093 0.1090
Step 4500659, time 9001.32 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000112, max 0.001661 (between atoms 2217 and 2219)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 34.6 0.1090 0.1091 0.1090
Step 4500660, time 9001.32 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000168, max 0.003118 (between atoms 3331 and 3330)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 34.1 0.1091 0.1093 0.1090
Step 4500664, time 9001.33 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000120, max 0.002250 (between atoms 3329 and 3328)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 39.4 0.1091 0.1090 0.1090
Step 4500665, time 9001.33 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000127, max 0.001588 (between atoms 3333 and 3332)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 35.9 0.1090 0.1090 0.1090
Step 4500669, time 9001.34 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000116, max 0.001965 (between atoms 3329 and 3328)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 32.1 0.1091 0.1092 0.1090
Step 4500670, time 9001.34 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000149, max 0.002709 (between atoms 3331 and 3330)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 41.6 0.1092 0.1093 0.1090
Step 4500671, time 9001.34 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000189, max 0.002999 (between atoms 3327 and 3326)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 36.6 0.1093 0.1093 0.1090
Step 4500672, time 9001.34 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000225, max 0.004804 (between atoms 3327 and 3326)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 4500686, time 9001.37 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000156, max 0.003574 (between atoms 3331 and 3330)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 30.9 0.1094 0.1094 0.1090
Step 4500687, time 9001.37 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000161, max 0.002976 (between atoms 3331 and 3330)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 39.3 0.1094 0.1093 0.1090
Step 4500688, time 9001.38 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000171, max 0.002600 (between atoms 3329 and 3328)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3331 3330 41.0 0.1093 0.1092 0.1090
Step 4500689, time 9001.38 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000127, max 0.002282 (between atoms 3328 and 3327)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3329 3328 36.2 0.1093 0.1091 0.1090
3331 3330 32.4 0.1092 0.1090 0.1090
Step 4500690, time 9001.38 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000133, max 0.002643 (between atoms 3331 and 3330)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3329 3328 35.7 0.1091 0.1090 0.1090
3331 3330 30.4 0.1090 0.1087 0.1090
Step 4500692, time 9001.38 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000373, max 0.007624 (between atoms 3329 and 3328)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3329 3328 47.9 0.1089 0.1082 0.1090
Step 4500693, time 9001.39 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000149, max 0.003023 (between atoms 3327 and 3326)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3329 3328 48.2 0.1082 0.1093 0.1090
Step 4500694, time 9001.39 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.080880, max 2.067793 (between atoms 3329 and 3328)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3329 3328 90.1 0.1093 0.3344 0.1090
3331 3330 90.0 0.1090 0.2852 0.1090
Wrote pdb files with previous and current coordinates
Step 4500695, time 9001.39 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 490.514956, max 15813.544922 (between atoms 3331 and 3330)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3323 3322 59.0 0.1610 2.3283 0.1610
3326 3323 92.9 0.1616 4.3197 0.1610
3325 3323 88.7 0.1479 2.3003 0.1480
3324 3323 118.7 0.1610 2.2779 0.1610
3327 3326 52.0 0.1362 21.8600 0.1360
1807 1808 90.0 0.1090 0.5027 0.1090
3332 3327 106.4 0.1399 31.1642 0.1390
3328 3327 92.3 0.1403 68.1702 0.1390
3330 3328 89.5 0.1399 34.3474 0.1390
3329 3328 95.1 0.3344 47.7915 0.1090
3336 3330 92.4 0.1405 179.8941 0.1390
3331 3330 89.6 0.2852 1723.7854 0.1090
3334 3332 96.7 0.1392 59.2178 0.1390
3333 3332 121.2 0.1090 10.6428 0.1090
3336 3334 90.0 0.1391 67.5634 0.1390
3335 3334 101.3 0.1091 29.9005 0.1090
3337 3336 96.8 0.1392 151.3580 0.1390
3338 3337 91.6 0.1531 134.4151 0.1530
3344 3338 86.4 0.1530 43.7928 0.1530
3339 3338 101.9 0.1470 37.5223 0.1470
3341 3339 92.7 0.1340 11.1102 0.1340
3340 3339 88.7 0.1000 7.2787 0.1000
3343 3341 105.7 0.1530 2.5647 0.1530
3342 3341 103.6 0.1230 2.6986 0.1230
3346 3344 82.0 0.1340 1.1837 0.1340
3345 3344 81.9 0.1230 0.9566 0.1230
3348 3346 88.9 0.1470 0.6030 0.1470
3347 3346 88.1 0.1000 0.3101 0.1000
3353 3348 82.2 0.1530 0.2466 0.1530
3349 3348 82.9 0.1530 0.2589 0.1530
3350 3349 44.2 0.1530 0.2128 0.1530
3355 3353 36.7 0.1340 0.1797 0.1340
3354 3353 36.8 0.1230 0.1639 0.1230
Wrote pdb files with previous and current coordinates
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 26195 on node node01
exited on signal 11 (Segmentation fault).
====================================================================================================
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