[gmx-users] Box Borders

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jul 5 02:17:09 CEST 2012

On 4/07/2012 6:17 PM, ifat shub wrote:
> Hello,
> I am running a simulation of a protein-protein complex using explicit
> solvent. (mdrun -v -deffnm run)
> I created a box for the simulation (d=5) using editconf:
> editconf -princ -f conf.gro -bt dodecahedron -d 5.0 -c -o box.gro
> I am using the option pbc=no in the run.mdp file.
> Can anyone explain what happens if the complex reaches the "walls" of
> the box?

The simulation system is always of infinite extent. You chose for it to 
be non-periodic. There are no walls in either case.


>   Does the complex return to the box with the enrgy gained from
> the collision? Can the complex cross the "walls"?
> Thanks,
> Ifat

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