[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 25 14:05:51 CEST 2011

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 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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