[gmx-users] How to confine a protein in a box?

Lee Soin nomadoro at gmail.com
Tue Oct 14 08:18:31 CEST 2008


I'm going to put two peptide chains in a box and study dimerization. I think
confining them in a box can reduce conformational search.

2008/10/14 Jochen Hub <jhub at gwdg.de>

> Lee Soin wrote:
> > Hello, all! I intend to simulate a protein confined in a box. Can anybody
> > tell me how to define a boundary, or a wall, in GROMACS? Thanks!
>
> As far as I know Berk has implemented walls in gromacs 4.0. Check the
> new mdp options. Are you sure that you do not want to use peridic
> boundary conditions?
>
> Best, Jochen
>
> >
> >
> >
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>
> --
> ************************************************
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
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-- 
Sun Li
Department of Physics
Nanjing University, China
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