From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Sat Apr 17 2010 - 08:40:16 CDT

Hi all

I have the following query regarding simulation using Desmond and pbc
tools in VMD

I kept my protein for simulation for 3ns duration but after 2ns
simulation it has started coming out of the simulation box and the
same thing happened with a friend of mine twice when he simulated his
protein for 3ns . In gromacs we can tackle the same problem by setting
the protein location to the centre of the box .. Can you tell me how
can I do this in using pbc tools in VMD.

It will be of great help if you respond to my query as soon as
possible as I have to submit my M.Sc. thesis on 26th April.

Details about my department :-

Centre For Bioinformatics
Pondicherry University
Puducherry -605014

Thanks

-- 
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Puducherry
India
Mob. +919962670525