AW: [gmx-users] About movie in GROMACS
frausch at ipb-halle.de
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 gromacs.org [mailto:gmx-users-bounces at 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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