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
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