[gmx-users] Regarding Production MD error
Emanuel Birru
Emanuel.Birru at monash.edu
Sun Aug 19 09:52:02 CEST 2012
It's a LINCS warning relayed to some of the bonding of the atoms, check them they are listed on the warning. Two things that I can suggest is that
1. If you are using bigger time steps make it smaller like 1fs.
2. If those atoms which make the problem are H atoms makes the heavy atom and rerun the simulation.
If you tell us more about your system you might get more help. You can get More info on the GROMACS website.
Cheers,
EB
Sent from my iPhone
On 19/08/2012, at 5:41 PM, "kirubakaran palani" <kirubakaran17 at gmail.com> 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.
>
> 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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