Question for 2D periodic boundary condition

From: Chin_Wei (
Date: Mon Sep 17 2007 - 09:18:13 CDT

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
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

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