[gmx-users] problem while running production md

[ansuman at physics.iisc.ernet.in]

dear gmx-users,

i am getting the following error message while running production md
(mpirun)......


Step 102, time 0.204 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 122.760095, max 2890.435059 (between atoms 5092 and 5090)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5079   5069   30.7    0.1532   0.1888      0.1522
   5081   5079   79.8    0.1056   0.2608      0.1335
   5080   5079   39.1    0.1237   0.1673      0.1229
   5083   5081   79.7    0.1459   0.8597      0.1449
   5082   5081   78.7    0.1016   0.1856      0.1010
   5098   5083   78.5    0.1532   0.7685      0.1522
   5085   5083   85.9    0.1537   1.9840      0.1526
   5084   5083   70.4    0.1097   0.4235      0.1090
   5088   5085   83.6    0.1536   2.4114      0.1526
   5087   5085   85.9    0.1098   1.5565      0.1090
   5086   5085   87.3    0.1099   1.2617      0.1090
   5088   5094   88.6    0.1535   3.0328      0.1526
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 5093 and 5094 at distance 6.570 which is
larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Warning: 1-4 interaction between 5091 and 5094 at distance 2.444 which is
larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Fatal error:
1 particles communicated to PME node 3 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

any suggestion to get rid of this problem........

Ansuman Biswas
Physics Department
Indian Institute of Science
Bangalore
India



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