[gmx-users] About movie in GROMACS
Mark.Abraham at anu.edu.au
Thu Mar 29 09:42:15 CEST 2012
On 29/03/2012 4:15 PM, rama david wrote:
> 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 ???
It depends. See suggested workflow here:
There is no general solution for an arbitrary trajectory to look nice.
There need not even be a solution for a specific trajectory to look
nice. Imagine a cluster of molecules from which one emerges, transits
the whole simulation cell including periodic boundary, and merges again
with the other side of the cluster. You cannot create a representation
of the trajectory that lacks jumps and has the cluster whole when it is
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