[gmx-users] About movie in GROMACS

[Mark Abraham]

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: 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. 
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 
whole.

Mark