[gmx-users] trjconv -pbc nojump
Reisser, Sabine (IPC)
sabine.reisser at kit.edu
Wed Sep 2 13:17:06 CEST 2015
Thanks for the reply, but I don't want the lipids to jump from one edge of the box to the other, which they do with this option, even though they remain complete.
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology
Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> im Auftrag von Ganesh Shahane <ganesh7shahane at gmail.com>
Gesendet: Mittwoch, 2. September 2015 12:19
An: gmx-users at gromacs.org
Betreff: Re: [gmx-users] trjconv -pbc nojump
Instead of using -pbc nojump, use -pbc whole.
On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) <
sabine.reisser at kit.edu> wrote:
> I want to use trjconv -pbc nojump to create a trajectory without box
> jumping of molecules. The molecules (lipids) also start to diffuse out of
> the box like they should, but in some a part of the molecule still jumps
> (as I could observe in xy direction), while the rest doesn't, leading to
> artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr
> file in the -s option, or a gro file (with only complete molecules), same
> I'd be glad if somebody could give me a hint.
> Dr. Sabine Reißer
> Theoretical Chemical Biology
> Institute of Physical Chemistry
> Karlsruhe Institute of Technology
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