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