[gmx-users] trjconv -pbc nojump

[Reisser, Sabine (IPC)]

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.

Cheers
Sabine



--
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

Hi Reisser,

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:

> Hi,
>
>
> 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
> result.
>
>
> I'd be glad if somebody could give me a hint.
>
>
> Cheers
>
> Sabine
>
>
>
> --
> Dr. Sabine Reißer
> Theoretical Chemical Biology
> Institute of Physical Chemistry
> Karlsruhe Institute of Technology
>
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Best Regards,
Ganesh Shahane
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