[gmx-users] what does the error mean

[Martina Bertsch, PhD]

>
> xiaoyi li wrote:
>
>> Hello,
>>
>> My system is composed from two proteins, two axt molecules and a box of
>> water. During the MD run by Gromacs, it is always stopped at 200ps or
>> less because of error.
>>
>> At the end of .log file, it shows:
>>
>> Constraint error in algorithm Lincs at step 10767
>>
>> t = 21.534 ps: Water molecule starting at atom 45552 can not be settled.
>> Check for bad contacts and/or reduce the timestep.Wrote pdb files 
>> with previous
>> and current coordinates
>> Grid: -2147483648 x -2147483648 x -2147483648 cells
>> Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 211]
>>
>> What should I do?
>>
>> Thanks a lot!
>>
>> xiaoyi
>>
> Greetings, Xiaoyi.
>
> You could try the energy minimization protocol with fully flexible 
> water molecules, i.e., add the following to the .top file:
>
> #include flexspc.itp
>
> Also, in the .mdp file set:
>
> constraints = none.
>
> Finally, emstep in .mdp should be small (0.001 per Marcos Villarreal, 
> see an earlier message in the archive).
>
> Martina Bertsch, Ph.D.
> Northwestern University
> Feinberg School of Medicine
> Molecular Pharmacology and Biological Chemistry
> 303 East Chicago Avenue
> Chicago, IL 60611
>
>>
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>
>