[gmx-users] simulation scattered

David van der Spoel spoel at xray.bmc.uu.se
Sat Jul 15 09:58:52 CEST 2006

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 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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