[gmx-users] -pbc nojump

[Tsjerk Wassenaar]

Hi Sara,

The problem is that your micelle is formed at the end of the
trajectory. To get what you want, you need to mirror the trajectory,
follow the procedure you followed, and mirror the resulting
trajectory. I posted a piece of python code for mirroring a trajectory
a while back: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061443.html

Hope it helps,

Tsjerk


On Wed, Dec 28, 2011 at 5:25 PM, mohammad agha <mra_bu at yahoo.com> wrote:
> Dear GROMACS users,
>
> I have a problem about trjconv -pbc nojump, I have 2 micelles in the end of
> my simulation. For analysis I should do three steps for micelle clustering
> at
> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering
> Steps 1 and 2 work good and when I view my trajectory after step2 by :
> ngmx -f a_cluster.gro -s a_cluster.tpr
> is viewed 2 micelles, but when I did step 3 (trjconv -nojump) and after do :
> ngmx -f a_cluster.xtc -s a_cluster.tpr
> has been created 1 micelle and reminder of monomers have been collected as
> some groups at different places.
> May I ask you to help me, please?
> Thank you
>
> Best Regards
> Sara
>
>
>
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-- 
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