From: Axel Kohlmeyer (
Date: Mon Sep 27 2010 - 10:32:58 CDT

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


> 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.


> Thanks.
> Regards,
> Joyce

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.