[gmx-users] simulation scattered

erwin berthier erwindownunder at gmail.com
Sat Jul 15 07:38:25 CEST 2006

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?
Erwin Berthier

PhD student
University of Canterbury
Electrical Engineering department
New Zealand
erwindownunder at gmail.com
+64 (0)3 3667001 + ext 7123

More information about the gromacs.org_gmx-users mailing list