[gmx-users] Re: problem while running production md

[Dr. Vitaly V. Chaban]

> 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


I think your system is not relaxed, so you are NOT actually running
"production md".

-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA