[gmx-users] Unknown arguement -e

[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


I tried using grompp -t traj.trr -time 500 -e ener.edr but it said unknown
arguement -e.  It also said this for tpbconv when I put -e.

I am using GROMACS version 3.1.4.


>> 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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