[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 25 16:06:28 CEST 2011

James Starlight wrote:
> Justin,
> I've found the same task of MSU's students :) They simulate membrane 
> formation without NPT stage ( after NVT they run production MD). From 
> they reports I've found that simplest membrane system could be formed 
> within 10-30 Ns.  But what about try to make such simulation in vacuum 
> at first without any water ? Might the bilayer been formed in such 
> conditions?
> Finally I have small question about pereodic boundaries of such bilayer 
> system.
> E.g I've done simplest system with water consisted of 8 lipid molecules 
> + some water.
> This is the representation of the system 
> http://i1209.photobucket.com/albums/cc394/own11/lipids8.png
> I want to simulate bilayer formation as well as concomitant hydrophobic 
> effect ( removing all water from formed bilayer)
> Does the PBC presented in that example ( 2.64196   2.64196   6.85002 for 
> 8 lipids) are enought for such lipid movement? It seems that more free 
> space aree needed for overal turn of lipid molecules. How I can 
> calculate exactly  PBC value required for my system ?

I agree that your system has insufficient space for any real movement without 
violating the minimum image convention.  Your system must have adequate room for 
any lipid to rotate in any direction, and be of sufficient size to accommodate a 
formed membrane, which will have dimensions dictated by the APL for the chosen 
lipid (and of course, the force field's ability to produce that value).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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