Holding molecules on one side of membrane

From: Omid Bavi (omidbavi_at_gmail.com)
Date: Sun Feb 04 2018 - 07:14:26 CST

Dear NAMD users,

I have a POPE bilayer and want to see the effect of some drug molecules
just on the one side of my membrane. At the beginning of the simulation,
the drug molecules are properly solvated in one side (e.g outer side);
However during the run, due to the periodic boundary of the system in 3D,
some drug molecules go from the upper boundary and come from lower
boundary. So I have some unwanted drug molecules on the inner side.
If anyone has any experience dealing with this kind of problem, please do


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