VMD-L Mailing List

From: Mihaela Drenscko (quo.physics_at_gmail.com)
Date: Wed Nov 27 2013 - 06:56:17 CST

Hi,

I would noy have written without doing first a preliminary research and
several tries.I tried RMSD trajectory tool and I saw that someone asked a
similar question and used this script:
*pbc wrap -centersel water -center com -compound residue -all*
Yet, I get errors in angle calculations.
Maybe I don't use the script in the correct way? I would appreciate
suggestions.

Thank you,

Mihaela

On Tue, Nov 26, 2013 at 8:04 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> Have you look at using PBCtools to wrap your waters back to the
> original unit cell? You can search the VMD-L list for many
> discussions of the use of pbctools...
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Tue, Nov 26, 2013 at 07:26:51PM -0500, Mihaela Drenscko wrote:
> > Hi,
> >
> > When I run water on graphite simulation, my water bulk drifts towards
> next
> > cell, such that at the end of the simulation I have part of the water
> in
> > one cell and part in another.
> > I have to do an analysis of the trajectories and the program I use
> doe not
> > read the part of the water molecules that are in the adjacent cell.
> > What can I do to keep all water molecule centered in one cell, such
> that
> > my program can real all trajectories?
> >
> > Thank you,
> >
> > Mihaela
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>