[gmx-users] Imaging in PBC simulations

Tamas Horvath hotafin at gmail.com
Mon Apr 24 15:56:58 CEST 2006

I wrote a program using bioJava, that recenters the protein in every
frame... that does the job quite nicely, but there maybe other options.

On 4/24/06, Martin LEPSIK <martin.lepsik at ibs.fr> wrote:
> Dear GROMACS users,
> I would like to ask you maybe a trivial question: What is the best way
> to image a protein with a ligand inside
> a triclinic water box?
> I run an MD in GMX-3.3 with nstcomm=1, "comm_grps" and "comm_mode" not
> set. I watch the movie in VMD,
> loading first a starting gro and than the trr. The problem is that the
> protein creeps out of the box (the same happens
> when using ngmx).
> I have tried various variants of post-processing using trjconv -fit
> (translation) -pbc (inbox, whole) -center (tric),
> groups for fitting: protein or system. But in any case, the result is
> the same.
> Could you please advice me how to solve this? Whether it is better to
> include some parameter for
> mdrun or to post-process in a different way?
> Looking forward to hearing from you.
> Yours sincerely,
> Martin Lepsik
> --
> --------------------------
> Martin Lepsik, Ph.D.
> Laboratoire de Dynamique Moléculaire (LDM)
> Institut de Biologie Structurale
> 41, rue Jules Horowitz
> 38027 Grenoble Cedex 1, France
> tel: +33-4-3878-4780
> e-mail: martin.lepsik at ibs.fr
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060424/553f1890/attachment.html>

More information about the gromacs.org_gmx-users mailing list