Periodic boundary condition in a membrane simulation

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Mon Feb 09 2009 - 17:28:38 CST

Hi

I am trying to run a md simulation with a protein embedded in water and
membrane bilayer with namd2.6 in linux. I only add water in the z-axis to
leave out the edges of the lipid bilayer so that the membrane extends in the
x,y direction with other cells. The md.in of the periodic boundary condition
(PBC) is set as the following:

# Periodic Boundary Conditions
cellBasisVector1 102.7 0 0
cellBasisVector2 0 101.0 0
cellBasisVector3 0 0 83.5
cellOrigin 0.88 1.65 -1.86
wrapAll on
wrapNearest on

After a short md run, the lipid molecules on the side start to flip randomly
which is a sign of no contact with other lipid in the neighboring cells. I
wonder if the way I set up the PBC is wrong. In addition, I wonder if there
is a way to visualize the periodic cells (with VMD preferably)? Any
suggestions will be appreciated. Thank you.

Eric

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