[gmx-users] Simulation crashing

[fsaadedi at staffmail.ed.ac.uk]

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
>
> 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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