[gmx-users] Measure contour area of bilayer undulation

Erik Lindahl lindahl at cbr.su.se
Fri Aug 31 22:42:31 CEST 2007


In principle you can calculate this from equations e.g. in Safran's  
book "Statistical Thermodynamics of Surfaces, Interfaces, and  

However, when we worked with this a few years ago we ended up in the  
conclusion that for the properties we were interested in, the  
"effective" area/lipid measured in experiments was better  
approximated by the cell dimensions including fluctuations. YMMV,  



On Aug 31, 2007, at 10:22 PM, Hwankyu Lee wrote:

> Dear gmx-users,
> This is not a question about Gromacs, but I wonder if I can hear  
> suggestions from here. I would like to measure contour area of  
> bilayer undulation.  If there is no undulation, area (area per  
> lipid) can be easily calculated by dividing XY area by number of  
> lipid.  But, in the lipid bilayer with undulation, how can contour  
> area (ultimately, area per lipid) be calculated ?  If there are  
> some suggestions about possibilities in Gromacs or other tools,  
> it'd be really appreciated.
> Thanks,
> best,
> Hwankyu.
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