[gmx-users] PBC

shahab shariati shahab.shariati at gmail.com
Tue Jun 8 09:23:28 CEST 2010

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.

Is there any other method or command which I could implement pbc in


Thanks in advance


Shahab Shariati wrote:

You can use other flags of trjconv command as follows:

Trjconv –f *.xtc –s **.tpr –o ***.xtc –pbc nojump –ur compact -center
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