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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