Re: Question for 2D periodic boundary condition

From: JC Gumbart (
Date: Mon Sep 17 2007 - 17:41:03 CDT

I can think of a couple things you can do:

1) something I've seen done in the past is to use a double bilayer
system, thus confining the molecules to the region between them.
However, they will still interact with both the top of one bilayer
and the bottom of another so it's only relevant if you're most
interested in something like diffusion across the bilayer.

2) Use tclbc to apply a force to the peptide anytime it reaches the
top boundary of the box. This might take a little bit of thought to
set up but should then be simple to run. There is even a tutorial to
help you get started with it:

On Sep 17, 2007, at 9:18 AM, Chin_Wei wrote:

> Dear NAMD users,
> We use NAMD to simulate the interactions of peptide-membrane bilayer.
> Our MD simulation system includes several short peptides and one
> membrane bilayer.
> When the 3D periodic boundary condition is turned on, some peptides
> may absorb on the upper membrane layer, but some may approach the
> other
> layer.
> In our study, we want peptides to interact with one layer ONLY rather
> than both layers.
> We guess people who are doing the peptide-membrane simulation may also
> have similar questions. We do not know whether there is any good trick
> implemented in NAMD which can solve this problem?
> To fulfill the requirement, we are considering to turn off the z-axis
> PBC or increase the thickness of water layer. However, these two
> approaches seem impractical in MD simulations.
> More and more people are doing the peptide-membrane simulations, there
> may have a good method developed to confine the peptide to interact
> with one specific layer only.
> Any comment or suggestion is welcome! Many Thanks.
> Chi-Wei Tsai
> National Central University
> Taiwan

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