VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jun 28 2012 - 17:09:09 CDT

On Thu, Jun 28, 2012 at 2:46 PM, Dian Jiao <oscarjiao_at_gmail.com> wrote:
> Hi VMDers,
>
> I was trying to load a trajectory in the format of xmol. The system consists
> a metal ion and 64 waters. In VMD, the metal ion appears at the corner of
> the box and some of the water o-h bonds are broken with OH on one side and H
> on the other side. I thought the pbc wrap command would fix this, but it
> didn't work as I expected. What is the right command to get everything
> wraped properly in a box centered at the metal ion?

the right way to do this is to use a proper file format
that also contains information about the simulation cell.
yours (xmol, xyz) doesn't, so you lose. there is no way
to get back information that you don't provide.

axel.

>
> DJ 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.