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

Lee Soin nomadoro at gmail.com
Fri Oct 10 16:00:28 CEST 2008

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.

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

> Boundary should not "precisely" be around the protein, otherwise some parts
> of the protein would "feel" other parts via the boundary.
> In general, if you apply periodic boundary conditions (PBC), take the
> dimensions as such so the protein would NOT feel the PBC.
> Say you have an unfolded protein (or a MD during which a protein unfolds)
> whose length is about 20 Angstroms, and you use no explicit solvent. You
> might not want to take the dimension of the box to be smaller they, say, 40
> Angstroms.
> Its just an example.
> Omer.
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
> On Fri, Oct 10, 2008 at 11:03, Lee Soin <nomadoro at gmail.com> wrote:
>> But the problem is: how to define a boundary?
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Sun Li
Department of Physics
Nanjing University, China
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