[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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