[gmx-users] bilayer area questions

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Wed Sep 14 01:25:30 CEST 2005

> 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

Catch ya,

Dr. Dallas Warren
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
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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