Re: Holding molecules on one side of membrane

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Feb 05 2018 - 11:18:56 CST

Hi Omid,

An alternative approach would be to make a two-membrane system (e.g. like what they show in 10.1016/j.bpj.2011.06.010), or to use a semi-periodic system using multilevel summation instead of PME (10.1016/j.bpj.2016.05.039).

-Josh

On 02/04/2018 08:13 AM, Giacomo Fiorin wrote:
Hi Omid, you need to apply a boundary potential to the molecule, using either tclForces or Colvars.

Giacomo

On Sun, Feb 4, 2018 at 8:14 AM, Omid Bavi <omidbavi_at_gmail.com<mailto:omidbavi_at_gmail.com>> 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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