[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Tue Oct 25 15:34:56 CEST 2011


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

E.g I've done simplest system with water consisted of 8 lipid molecules +
some water.
This is the representation of the system
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 ?


2011/10/25 Justin A. Lemkul <jalemkul at vt.edu>

> James Starlight wrote:
>> Justin,
>> Could you tell me if I want to simulate self-organization of the pure
>> lipid bilayer starting from the initial random placed molecules in water.
>> Does this simulation need in pre-md NVT and NPT equilibration?
> Some form of equilibration is always required.
>  What the average time for NPT? I think that If this stage should occur it
>> must be consist of long ( tens of NS ) preequilibration.
> Temperature and pressure will likely converge within a few ns, but the
> simulation is not equilibrated until the membrane has formed, I would say.
>  This is a process that can take hundreds of ns, or even us.  Check the
> literature for established protocols; there are reports of bilayer
> self-assembly already published.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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