AW: [gmx-users] About movie in GROMACS

Rausch, Felix frausch at
Thu Mar 29 08:55:06 CEST 2012


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-bounces at [mailto:gmx-users-bounces at] 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 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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