Periodic boundary conditions in membrane simulation

From: jouko_at_uchicago.edu
Date: Mon Aug 31 2009 - 11:56:22 CDT

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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