[gmx-users] Imaging in PBC simulations

[Jochen Hub]

Martin LEPSIK wrote:

> Dear GROMACS users,
>
> I would like to ask you maybe a trivial question: What is the best way 
> to image a protein with a ligand inside
> a triclinic water box?
>
> I run an MD in GMX-3.3 with nstcomm=1, "comm_grps" and "comm_mode" not 
> set. I watch the movie in VMD,
> loading first a starting gro and than the trr. The problem is that the 
> protein creeps out of the box (the same happens
> when using ngmx).
>
> I have tried various variants of post-processing using trjconv -fit 
> (translation) -pbc (inbox, whole) -center (tric),
> groups for fitting: protein or system. But in any case, the result is 
> the same.
>
> Could you please advice me how to solve this? Whether it is better to 
> include some parameter for
> mdrun or to post-process in a different way?
>
> Looking forward to hearing from you.
>
> Yours sincerely,
>
> Martin Lepsik
>
You can either
 use comm_grps = Protein and comm_mode = Linear
 or
use trjconv with the -fit option and fit your protein on the starting 
position after finishing the simulation.

Cheers, Jochen


-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
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