[gmx-users] Simulation crashing

[David van der Spoel]

On Fri, 2005-09-02 at 13:33 +0100, fsaadedi at staffmail.ed.ac.uk wrote:
> Quoting fsaadedi at staffmail.ed.ac.uk:
> 
> > Dear David,
> >
> > My tau_p is 5.0 5.0 5.0 in my mdp file.  How much is a reasnoble increase in
> > tau_p?  I know how to calculate the density of my system at the start of the
> > simulation using editconf.  But how can I recalculate the system after a
> > simulation crash?  Farid
tau_p - 20 for anisotropic.
Use g_energy.

> >
> > Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
> >
> >> 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
> >>> SCOTLAND
> >>>
> >>> _______________________________________________
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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://xray.bmc.uu.se/~spoel
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >>
> >> _______________________________________________
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> >>
> >
> >
> >
> > _______________________________________________
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> 
> 
> 
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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://xray.bmc.uu.se/~spoel
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