[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

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

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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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