[gmx-users] About the "mdrun" err's information

[David van der Spoel]

Aurum Bai wrote:
> Dear everyone,
> 
> When I input the command:"mdrun -v -deffnm em", some err happen and some
> information is as below:
> 
> ---------------------------------------------------------------------
> Program mdrun, VERSION 3.3.3
> Source code file: nsgrid.c, line: 226
> 
> Range checking error:
> Explanation: 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.
> 
> Variable ci has value -2147483648. It should have been within [ 0 .. 1728 ]
> ---------------------------------------------------------------------------
> 
> What's wrong? How to solve it?

Have you read the message?
> 
> Thanks 
> 
> Aurum
> 
> 
>       
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se