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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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