[gmx-users] Simulation of a protein confined in a box

Suman Chakrabarty suman at sscu.iisc.ernet.in
Sat Oct 11 09:26:23 CEST 2008

Possibly what he is interested in is a system WITHOUT PBC? I don't think
with PBC the system is really "confined", since there is no true wall to
reflect the colliding molecules. Thus to study the effect of real
confinement, it is necessary to remove PBC and impose reflective
boundary conditions. I am only guessing! :)


Omer Markovitch wrote:
> In short - you can apply PBC in all directions (XYZ) by choosing the
> proper keyword in the .mdp file, I believe the box dimensions are
> defined in .gro file.
> Omer.
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
> On Fri, Oct 10, 2008 at 16:00, Lee Soin <nomadoro at gmail.com
> <mailto:nomadoro at gmail.com>> wrote:
>     Maybe I didn't put it clearly. My intention is to simulate a protein
>     confined in a box, and the problem is that I don't know how to
>     define a boundary, or a wall, in GROMACS.
> -- 
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