[gmx-users] area per headgroup for lipid

[Dallas Warren]

> > Also, I try to use "g_sas" to calculate the hydrophilic solvent
> > accesibility area. the Index group that I set include all the lipids in the
> > system, the results show at at 0s, the hydrophilic area is 1663.18nm^2, if
> > I total have 256 lipids, then the SAS for per lipid is 6.49nm^2. It is far
> > from the per lipid headgroup area: ~0.61nm^2.

It would probably be advantageous for you to visualise the sas using 
something like Surf representation in VMD.  That will clearly show you why 
it is so large (it is the surface accessible to solvent and since the 
molecules are bumpy, then it is significantly larger than the x-y cross 
sectional area of the molecule).

Catch ya,

Dr. Dallas Warren
Research Fellow
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 9083
--------------------------------------------------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040611/ebb1eed7/attachment.html>