[gmx-users] Range checking error

[David van der Spoel]

Yanzi Zhou wrote:
> Dear Gromacs-Users,
> 
> Can anybody help me?
> 
> When I do 1 ns NTP MD simulation using version 3.3.2 on 4 or 6 processes
> with double precision gromacs compiled by Intel compiler on x86_64
> GNU/Linux, it was crashing at about 100 ps with a message:
> 
> -------------------------------------------------------
> 
> Program mdrun_mpi_d, VERSION 3.3.2
> 
> 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 4421. It should have been within [ 0 .. 4212 ]
> 
> -------------------------------------------------------
> 
> 
> But it can be finished when I use 1 or 2 processes, or use cut-off for
> electrostatics instead of PME, or for a NVT system, or with single
> precision gromacs. I have noticed the bug #167 on Bugzilla, and modified
> routine stat.c, but it did no help, and actually I didn't write to XTC
> file. Maybe, there are still bugs for double precision gromacs?

More likely the compiler. Please retry with gcc.

> 
> 
> Thanks for any help.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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