[gmx-users] PBC

ms devicerandom at gmail.com
Wed Jun 2 20:19:20 CEST 2010

On 02/06/10 18:48, Morteza Khabiri wrote:
> Dear users
> I have a dimer protein in the water box. It was run for 30ns.
> during the simulation dimer split to two monomer. This things happen bc of
> PBC. ( I checked it by vmd pbc option )
> to have a two monomer together during trajectories (for visualization)
> I have used the following command:
> trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol
> but it is not working.

Not working *how*? that is, what is output? .tpr and .xtc don't look 
like sensible file parameters.

> Is there any other method or command which I could implement pbc in
> trajectory.
> Thanks in advance
> Morteza

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