[gmx-users] a flat plane boundary condition

David spoel at xray.bmc.uu.se
Wed May 25 18:47:54 CEST 2005

On Wed, 2005-05-25 at 12:30 -0400, Beckett W Sterner wrote:
> 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?
You can freeze atoms in one, two or three dimensions. Check mdp options
on www.gromacs.org
> Thanks,
> Beckett
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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