[gmx-users] RE: Error in mdrun

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 30 17:18:17 CEST 2010

Nimesh Jain wrote:
> Hi,
> I keep getting the following error when I do mdrun:
> During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> I moved the particles sufficiently apart so that there are no overlaps. 
> I still get this error. Can someone tell me what else can I do?
> Please let me know if you need any other info.

An .mdp file, a description of your system, and a list of commands that shows 
how you built it would be required to get any useful advice.  Otherwise, the 
standard advice is (as always) found here:


Troubleshooting tips are listed there.


> Thanks,
> Nimesh


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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