VMD-L Mailing List
From: Parul tew (parultew_at_gmail.com)
Date: Sun May 22 2011 - 05:02:18 CDT
- Next message: Axel Kohlmeyer: "Re: Non-cuda version of VMD on Linux?"
- Previous message: Parul tew: "problem in overlapping atoms"
- In reply to: Parul tew: "problem in overlapping atoms"
- Next in thread: Ajasja Ljubetič: "Re: problem in overlapping atoms"
- Reply: Ajasja Ljubetič: "Re: problem in overlapping atoms"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Axel Kohlmeyer: "Re: Non-cuda version of VMD on Linux?"
- Previous message: Parul tew: "problem in overlapping atoms"
- In reply to: Parul tew: "problem in overlapping atoms"
- Next in thread: Ajasja Ljubetič: "Re: problem in overlapping atoms"
- Reply: Ajasja Ljubetič: "Re: problem in overlapping atoms"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]