[gmx-users] problem while running production md

[Justin A. Lemkul]

ansuman at physics.iisc.ernet.in wrote:
> 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........
> 

Please search the Gromacs website, where this issue is discussed in some depth, 
and/or search the list archive to find any of the thousands of posts where this 
issue has been solved before.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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