[gmx-users] Energy Minimization Problem

X.Periole X.Periole at rug.nl
Mon Apr 17 14:36:06 CEST 2006

On Mon, 17 Apr 2006 08:21:35 -0400 (EDT)
  "Robson P. S. Peguin" <ao8215 at wayne.edu> 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.


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