VMD-L Mailing List

From: dimka (newyorkdimka_at_gmail.com)
Date: Mon Nov 07 2005 - 13:10:20 CST

Hello All,

How do you know that lipids in your system are equilibrated??? You
can look at the average lipid area, protein-lipid interactions, and at
the lipid order parameter for each H-C-H group.

The script to calculate lipid order parameter had been posted to this
list few weeks ago, while I couldn't find any scripts to calculate
lipid area. Does anyone have such script?

While the problem may seem trivial for the pure lipid system, it is
not for the protein-lipid system. You can take the total area of your
system, subtract the protein area to obtain the lipid area and then
divide by the number of lipids in either the top or bottom membrane
leaflet. But often estimating the area of the protein is very crude
and as a result you tend to either over- or underestimate the lipid
area. You can also take a single lipid and look at its area, but I'm
not sure what atoms one should look at. Because of the flexibility of
the hydrocarbon chains I would think they are excluded from the
calculations, but not sure. Can anyone point me to a formal
definition of a "Lipid Area"?

Thanks.