[gmx-users] pbc = xy

Jennifer Rendell rendell at cs.mun.ca
Wed May 4 15:48:58 CEST 2005

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?

Thank you, Jennifer

Jennifer Rendell
Department of Biochemistry
Memorial Unversity of Newfoundland
St. John's, Newfoundland & Labrador


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