[gmx-users] bilayer area questions

[Dallas B. Warren]

> 1) Is it normal for a lipidbilayer to EXPAND after 
> equilibriation? (From 5.5 by 5.4 to 7.4 to 7.8, NPT
> compling)

Depends on large number of factors, main one being whether the starting
bilayer is actually at the correct density/head group area or not.  If
too small, then of course it will expand until it reaches around the
equilibrium area.

> 2) How does one calculate the area per lipid ? (is it
> as simple as multiply length of box x by box y and
> divide by number of lipids?)

That is the standard way to do it, and from what I can tell, pretty much
the only way.

> 3) How do i deal with the fact that my box size is
> same as original, but system has expanded, if i want
> to calculate the area per lipid?

How can the box size be the same as the originaly, when infact you have
stated that the dimensions of the box in the x-y plane has actually
expanded?

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
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a nail.