AW: [gmx-users] About movie in GROMACS

lloyd riggs lloyd.riggs at
Thu Mar 29 09:19:54 CEST 2012

>From my limited experience,

...Also, VMD makes this easier.  I learned the hard way to center on a molecule when making the initial box in editconf.  Otherwise varied combinations of the -mol, -pbc , -nojump -center options usually work, but never consitent at least for me.  Still, if its 4 small molecules it might not make a difference if the other 3 keep moving out of the box.

The only differences I noticed in analyzing these was with distances, and geometric math functions, in which case you would have to analyze each moleucle centered in the .trj (ie 3-4 different centered versions of the same initial .trj) seperat. All the energy and force values were independent of this though.

Good luck

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Thu, 29 Mar 2012 06:55:06 +0000
> Von: "Rausch, Felix" <frausch at>
> An: \'Discussion list for GROMACS users\' <gmx-users at>
> Betreff: AW: [gmx-users] About movie in GROMACS

> Hi.
> 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 ???

NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone!                                  
Jetzt informieren:

More information about the gromacs.org_gmx-users mailing list