Hi. Take a look at the "-center" flag of trjconv. Together with "-pbc" (and maybe also "-ur") it should be possible to center your molecules of interest in the middle of the simulation cell.
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von rama david Gesendet: Donnerstag, 29. März 2012 07:18 An: Discussion list for GROMACS users Betreff: [gmx-users] About movie in GROMACS HI Gromacs Friends, I complete one simulation for 4 different molecule placed apart in box of dimension 4 4 4 .. when I used the trajectory I saw the one molecule interact with each other but they are getting broken because of box..(Some part protruding from other side). To see movie I used the command 1. trjconv -s ..tpr -f ..xtc -o movie.pdb -pbc nojump -dt 10 The molecules moving apart without any interaction 2. trjconv -s ..tpr -f ..xtc -o movie.pdb -pbc whole -dt 10 The molecules are interacting in cell .. but because of periodic cell , near the cell boundary the molecule interaction get remove and molecules come in cell from other side.. ( I know it is because of periodic boundary condition ..one goes from right hand side come in cell through left hand side ) To see the four molecule interacting each other near also cell boundary , what command I have to use ???
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