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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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