[gmx-users] Simulation crashing

[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

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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