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

Lee Soin nomadoro at gmail.com
Sat Oct 11 14:40:45 CEST 2008

This seems to me a very complicated realization. Why doesn't GROMACS provide
an easy way for wall simulation?

2008/10/11 Omer Markovitch <omermar at gmail.com>

> 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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Sun Li
Department of Physics
Nanjing University, China
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