[gmx-users] Re: Measure contour area of bilayer undulation

[Erik Lindahl]

Hi,

On Aug 31, 2007, at 11:02 PM, Hwankyu Lee wrote:
>
>
> Thank you very much for your suggestion in the gromacs forum, but I  
> may not understand your explanation completely.  In the small  
> bilayer, there is no fluctuation, so area/lipid can be calculated  
> based on the cell dimensions.  But, in the big bilayer, area/lipid  
> can be much larger than that obtained from XYarea/lipid number  
> because of undulations.

First, try to keep the discussions on the list so the answers make it  
to the archive :-)

> Could you explain more details about reasons that area/lipid in the  
> big bilayer can be calculated better based on cell dimensions?

My point was rather the opposite - when people measure area/lipid in  
the lab on bilayer slabs there will be undulations present since they  
are typically not under tension. We discussed this with John Nagle a  
couple of years ago, and came to the conclusion that you should not  
try to compensate for it. This is one of the reasons you get more  
accurate results for larger systems.

If you still want to derive it (the error is in the order of 1%,  
IIRC) you should start with the works of Nagle & Safran!

Cheers,

Erik 
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