VMD-L Mailing List

From: Parul tew (parultew_at_gmail.com)
Date: Sun May 22 2011 - 05:02:18 CDT

 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