[gmx-users] adding a weak harmonic potential on one box side

Jennifer Rendell rendell at cs.mun.ca
Wed May 4 15:49:22 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 slip 
over to the opposite side.

How difficult is it to add a weak harmonic potential to one side of the 
box to keep the waters on their side. 

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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