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

Jochen Hub jhub at gwdg.de
Mon Oct 13 18:25:50 CEST 2008

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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