[gmx-users] About movie in GROMACS

[rama david]

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 ???
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120329/a019018e/attachment.html>