VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 27 2010 - 10:32:58 CDT

On Mon, Sep 27, 2010 at 5:58 AM, Joyce Tan <joyce.tankh_at_gmail.com> wrote:
> Hi.

joyce,

> I've extended my 5ns MD simulation for another 10ns using GROMACS. After the
> simulation completed, i've converted some of the trajectory frame into pdb
> format and the protein appear to break into parts as in the attached jpeg
> file. When I look back to the trajectory file, the protein is broken into
> parts, too with long lines connecting the parts. May I know why this occur
> and how to solve it?

this looks (in both cases) like a typical case of a
molecule moving across periodic boundaries while
coordinate wrapping is into the principle simulation
cell is active.

i suggest you meditate a little about what periodic
boundary conditions mean to an MD simulation and
then have a look at the pbctool plugin and the search
the mailing list archives about strategies to recombine
the protein. there are a number of different options and
their drawbacks and benefits depend on what you
plan to do with the coordinate data after the transformation.

cheers,
    axel.

>
> Thanks.
>
> Regards,
> Joyce
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.