Re: Holding molecules on one side of membrane

From: Giacomo Fiorin (
Date: Sun Feb 04 2018 - 09:07:30 CST

Hi Omid, you need to apply a boundary potential to the molecule, using
either tclForces or Colvars.


On Sun, Feb 4, 2018 at 8:14 AM, Omid Bavi <> wrote:

> 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
> reply.
> Cheers,
> Omid

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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