[gmx-users] RE: Error in mdrun

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Troubleshooting tips are listed there.

-Justin

> Thanks,
> Nimesh
> 

-- 
========================================

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

========================================