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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