[gmx-users] Fwd: -pbc nojump

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 27 10:45:08 CEST 2010

Hi Leila,

Maybe you're better off trying:

1. trjconv -pbc nojump       # choose system for output
2. trjconv -center -pbc mol # choose protein/dna for centering, system
for output

Centering is done before removing PBC, so you should be safe with two passes.
You might also want to play with -ur to get the best looking
representation. Just try some things and see what it does :)

Hope it helps,


On Wed, Oct 27, 2010 at 10:05 AM, leila karami <karami.leila1 at gmail.com> wrote:
> Hi Carsten
> Thanks for your answer. You got my case very well.
> I understand your mean as follows:
> 1)      Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol  (output group=water)
> 2)      Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group
> =protein-dna)
> Is that true?
> You said, (Then overlay both results in the visualization program). How?
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> 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/Support/Mailing_Lists

Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list