Re: [gmx-users] Regarding Production MD error

Sun, 19 Aug 2012 01:25:00 -0700 

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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