[gmx-users] Regarding Production MD error
Mark Abraham
Mark.Abraham at anu.edu.au
Sun Aug 19 10:24:26 CEST 2012
On 19/08/2012 5:40 PM, kirubakaran palani wrote:
> 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.
There are lots of possible reasons, which you'd have found a discussion
about if you'd followed the URL in your error message.
Mark
>
> 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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