From: Ajasja Ljubetič (
Date: Sun May 22 2011 - 05:52:14 CDT

Have a look at the membrane tutorial. It show how you can use VMD to
delete overlapping molecules.


On Sun, May 22, 2011 at 12:02, Parul tew <> wrote:

> Dear VMD users,
> I am using gromacs for simulating the protein in memnbrane. I designed a
> system containing protein, lipid membrane (dppc), water (spc), ions, when I
> try to minimize the system the potential energy is very high and there are
> infinite forces, that indicates atomic overlap between some elements of the
> system that I am not able to resolve. The environment around atom 1417 is
> problematic i.e. Maximum force = inf on atom 1417
> I think that there is some kind of overlap between protein and membrane ie
> there must be some lipid molecule trapped in the system.
> Can anyone suggest how can I diagnose why Its happening and how can I solve
> this problem using VMD.
> The atom 1417 is a CB atom of the protein.
> Parul