[gmx-users] Fwd: mdrun error

Amir Marcovitz amarcovitz at gmail.com
Mon Jan 4 17:20:25 CET 2010

---------- Forwarded message ----------
From: Amir Marcovitz <amarcovitz at gmail.com>
Date: Mon, Jan 4, 2010 at 6:18 PM
Subject: mdrun error
To: gmx-users-request at gromacs.org


my system is composed of 2 molecules that are arranged in a lattice: i.e.,
each molecule is represented by 4 atoms (which are charged) and organized in
a square lattice.

bonds, angles and dihedrals connect the 4 atoms on each lattice.

i want to simulate the 2 'plates' such that they are parallel so i added 90
degrees, inter-lattice angles between selected atoms in the system to the
[angles] section in the *.top file
the processing with grompp worked fine but the mdrun aborted with the
following error:

Program mdrun, VERSION 4.0.5
Source code file: nsgrid.c, line: 348*
*Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.*
beforehand the following massages poped-up:

* t = 2.954 ps: Water molecule starting at atom 9891 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates*
and* *
*Step 1478  Warning: pressure scaling more than 1%, mu: 1.95218 1.95218
does anyone has a clue of what is wrong?
Thanks, Amir
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