[gmx-users] PBC

[shahab shariati]

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

trajectory.



Thanks in advance



Morteza







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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