Re: Periodic boundary conditions in membrane simulation

From: Joshua Adelman (
Date: Mon Aug 31 2009 - 12:24:14 CDT

Hi Jouko,

I don't have any experience with simulating membrane systems, but I
remember coming across this paper from the Baker lab that might help:


On Aug 31, 2009, at 9:56 AM, <> <>

> I am planing on running a md simulation of a membrane. I want
> different ion concentrations on different sides of the
> membrane. My concern is that if I apply periodic boundary
> conditions ions will be able to diffuse from the top of
> simulation box to the bottom of the simulation box and I will
> not have a difference in the concentration of the ions. I
> thought that maybe I should create a wall with Tcl boundary
> conditions, or use two membranes, instead of one. I searched
> around and could not find anything that said periodic boundary
> conditions should be different for membrane simulations. I
> asked someone in my group and he said that I did not have to
> worry about this, and all I needed to do was turn wrap off. I
> disagreed with this. Eventually we decided to ask the namd
> mailing list. I would appreciate any advice on how to set up
> the simulation. I would also like someone to confirm or deny
> whether molecules can move from the top of the simulation box
> to the bottom, if periodic boundary conditions are applied
> regardless of whether wrap is on or off.
> Thanks,
> Jouko

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