From: Hitesh Patel (hiteshpatel379_at_gmail.com)
Date: Tue Apr 24 2012 - 11:34:00 CDT

Hi Chirag,
Use following command and.. whatever the selection you want to keep
at center, take that as *$sel1*

pbc wrap -compound fragment -center com -centersel $sel1

Regards,

Hitesh Patel

On Tue, Apr 24, 2012 at 7:04 AM, Chirag Vora <chirag740_at_gmail.com> wrote:

> Hi, I loaded my Desmond trajectories to VMD. When I visualize the
> simulation, I see the protein runs out of the water box. How do I center
> all atoms?
>
> In schrodinger's maestro there is a function "center atoms". Is there an
> equivalent function in VMD? How do I use it?
>
> --
> Chirag V. Vora
> Department of Pharmacoinformatics<http://niper.gov.in/depart.htm#Pharmacoinformatics>
> ,
> Block - A, Bioinformatics Infrastructure Facility,
> National Institute of Pharmaceutical Education and Research<http://niper.gov.in>(NIPER)
> Sector 67, S.A.S. Nagar,
> Punjab (INDIA) - 160 062,
>
> Phone: +91-9814187740
>
>