[gmx-users] Simulation crashing

Farid Sa'adedin fsaadedi at staffmail.ed.ac.uk
Fri Sep 2 12:44:01 CEST 2005

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 ).

If anyone can provide suggestions for this problem it would be most appreciated.


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
Edinburgh EH9 1QH

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