[gmx-users] pbc = xy

[David]

On Wed, 2005-05-04 at 11:18 -0230, Jennifer Rendell wrote:
> Dear Fellow Users, 
> 
> I am modelling a system of a lipid monolayer and water (on the headgroup 
> side). I am considering ways to prevent the water from jumping, via 
> periodic boundary conditions, over to the chain side of the layer.
> 
> I have had no success using position restraints on a separately
> defined layer of water near that box side. The water molecules still pop
> over to the opposite side.
> 
> How difficult is it to modify the gromacs code to keep periodic boundary
> conditions in the x and y directions, but not have it in the z direction.
> 
> Where would I start this kind of modification, if it is feasible?

A simple alternative is to add a vacuum layer by extending the box by
twice its length. 
> 
> Thank you, Jennifer
> 
> --
> Jennifer Rendell
> Department of Biochemistry
> Memorial Unversity of Newfoundland
> St. John's, Newfoundland & Labrador
> 
> 709-737-6733
> 
> 
> 
> 
> 
> 
> 
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-- 
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
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