[gmx-users] Simulation crashing

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 2 13:01:35 CEST 2005

On Fri, 2005-09-02 at 11:44 +0100, Farid Sa'adedin wrote:
> Dear Users,
> I am currently doing a simulation of a drug interacting with a bilayer.  I am
> trying to do a 5ns simulation.  Before I start the simulation I energy minimise
> the my system several times and equilibrate my system for about 30ps.
> When I start the simulation it crashes after 0.5ns, it gives an error message mu
> pressure scaling.
> I have noticed when I run the simulation on ngmx my box size decreases as the
> simulation goes on.  As a result part of my bilayer is going out of the box.  I
> am presuming that is causing my system to crash.  Is there anyway to prevent the
> box from automatically shrinking during the simulation? Any other suggestions
> you can give me to get my simulation to run for 5ns.
> I have tried to use tpbconv but as I am unfimiliar with this program I have had
> no success.  ( tpbconv -f traj.trr -s topol.tpr -time 520.40 ).
try grompp -t traj.trr -time 500 -e ener.edr 
with a longer tau_p in your mdp file.
Shrinking is normal until equilibrium is reached, but check the density
of your system.
> If anyone can provide suggestions for this problem it would be most appreciated.
> Farid
> Farid Sa'adedin
> Membrane Biophysics Laboratory
> Department of Veterinary Biomedical Sciences
> College of Medicine & Veterinary Medicine
> Royal (Dick) School of Veterinary Studies
> University of Edinburgh
> Summerhall
> Edinburgh EH9 1QH
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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://xray.bmc.uu.se/~spoel

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