[gmx-users] simulation scattered

[David van der Spoel]

erwin berthier wrote:
> Hello,
> I am trying to simulate a vesicule formation in water and it runs well
> on my laptop. I tried to run it on our cluster (gromacs was installed
> in my local directory) and something strange happens that I have
> trouble explaining, which made the search for already existing
> questions difficult.
> It is as if the lipids get packed to one side of the box and all the
> bonds split apart ; that happens instantly, so I assume that it is not
> a problem of the simulation engine, but rather of file reading.
> Can this happen if grompp or mdrun misses a file, or doesn't find a file?
> Thanks,
Do you mean that molecules are broken, or that they happen to be in a 
corner of the box? You can shift the center of mass of the lipids with 
editconf and put the lipids in the center of the box if you wish.

-- 
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://folding.bmc.uu.se
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