Amir Marcovitz wrote:
---------- Forwarded message ----------
From: *Amir Marcovitz* <[email protected] <mailto:[email protected]>>
Date: Mon, Jan 4, 2010 at 6:18 PM
Subject: mdrun error
To: [email protected] <mailto:[email protected]>
Hi,
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
1.95218*
**
does anyone has a clue of what is wrong?
All of these messages indicate that your system has become unstable, for which
there could be a number of reasons (insufficient minimization/equilibration,
lousy parameters, inappropriate .mdp settings, etc). For more detailed advice,
consult the wiki:
http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
If you need further help, post the procedure you have used to prepare the
system, the outcome of energy minimization, and your .mdp file.
-Justin
Thanks, Amir
--
========================================
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
========================================
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