[gmx-users] a flat plane boundary condition

[David]

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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++