RE: transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin

From: Zumot, Elia Nabil (
Date: Mon Feb 18 2013 - 11:49:35 CST

Hi Izhar,

There is no such protein where you have the same length of hydrophobicity everywhere at the surface (laterally or otherwise).
After equilibrating the system for a few nanoseconds you should be able to see how non-uniform your membrane becomes and how it adapts to the protein structure and surface hydrophobicity/philicity.


Elia Zomot, PhD
Computational and Systems Biology Department
School of Medicine, University of Pittsburgh
3089 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
Voice: 412 624 8699 - Fax: 412 648 3163
From: [] On Behalf Of Izhar Karbat []
Sent: Monday, February 18, 2013 12:26 PM
Cc: Yehu Moran; Maya Gur
Subject: namd-l: transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin

Dear NAMD users,

I am simulating a membrane system containing an ion channel embedded in a POPC bilayer. The hydrophobic thickness of the ion channel (according to the OPM database) is 27A. The membrane patch, generated with the membrane-builder plugin has hydrophobic thickness of ca. 31A. As a result, several extracellular segments of the channel which are expected to be solvent exposed, are facing a lipid. While this does not seem to affect the simulation stability over a few ns period, i'm afraid that longer runs might get skewed by the imperfect placement of the membrane. As quite several membrane proteins deviate from the "canonic" hydrophobic thickness of ~30A, and since the membrane plugin does not offer control over the bilayer thickness,
i hope that one of you might have encountered a similar problem in the past and may share is ideas concerning possible solutions.



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