[gmx-users] Fwd: -pbc nojump
tsjerkw at gmail.com
Wed Oct 27 10:45:08 CEST 2010
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
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
> Is that true?
> You said, (Then overlay both results in the visualization program). How?
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Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
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