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

[Omer Markovitch]

Oh, I didn't read carefully.
My suggestion would be, perhaps, to physically put atoms on the sides of the
box (possibly, fill each side completely), and to place on them very high
repulsion.
You might want to freeze them up, and exclude their self interactions from
the energy calculation.

Good guess Suman. Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty
<suman at sscu.iisc.ernet.in>wrote:

> 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! :)
>
>
> --Suman.
>
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