[gmx-users] a flat plane boundary condition

Jason de Joannis jdejoan at emory.edu
Thu May 26 18:10:26 CEST 2005

You can tether the protein's terminal atom to some point in space
using a gromacs "constraint". The best way to simulate a wall or plane
is to use a sharp repulsive external potential - most frequently the
planar analogue of Lennard-Jones. Eg: for a z=0 plane use the
potential 1/z^9. This has not been implemented in Gromacs as far
as I know - although I for one would like to have it. To add it yourself
would require a few lines in the do_force() routine.


Jason de Joannis, Ph.D.
Emory University
1515 Pierce Dr, Atlanta, GA 30329
Phone: (404) 712-2983
Email: jdejoan at emory.edu

> Date: Wed, 25 May 2005 12:30:12 -0400 (EDT)
> From: Beckett W Sterner <bsterner at MIT.EDU>
> Subject: [gmx-users] a flat plane boundary condition
> To: gmx-users at gromacs.org
> Hi,
>   I'm interested in doing a simple simulation of how a protein folds as it
> slowly emerges from a pore through a cell membrane.  I unfortunately do
> not have a crystal structure for the pore, and would like to keep
> computational costs to a minimum, so I'm interested in running an MD
> simulation on the protein where one end is fixed to a flat plane with a 2d
> periodic boundary condition.  Is there a way to implement this in GROMACS,
> perhaps using a force field?
> Thanks,
> Beckett

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