On Mon, 17 Apr 2006 08:21:35 -0400 (EDT)
"Robson P. S. Peguin" <[EMAIL PROTECTED]> wrote:
Hi everybody,
I'm trying to simulate an interfacial system using
Gromacs. My simulation box has water in one side and
hydrofluorocarbon in the other side. This system was
successfully tested using DL-POLY simulation package
previously. Also, the box containing pure
hydrofluorocarbon worked fine using Gromacs. However,
when I try an energy minimization simulation with the
interfacial system, after a couple of steps (~400), the
geometry of the hydrofluorocarbon changes. I mean, the
molecules begin to lose bonds or atoms. It didn't
collapse the box yet, but I can see from a visualization
package that the molecules are distorted. I tried to
decrease the timestep unsuccessfully. If you have any
suggestions, I'll be happy to know them.
You should check your topology: bond definition from what
you describe lokks necessary.
XAvier
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