[gmx-users] g_sas, what's it all about?

[Peyman Yamin]

Hello List!

I use g_sas to calculate the solvent accessible surface area of some 
amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if the 
hydrophilic part is somehow not recognized, or these terms mean different 
things in g_sas context? For Triton, for instance, a big surface is 
hydrophilic, to my knowledge!

I use ffG43a1. Is it a strange behavior to calculate SAS from a UA trajectory? 

How is the DGsolv calculated by g_sas? and the areas ? which algorithm? where 
is the code?

Is there any program with which one could calculate the volume enclosed by SAS 
resulted from g_sas?

I see different posts in the mailing list addressing the accuracy of g_sas! 
Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?

Any comment is truthfully appreciated :)

Peyman


P.S. Edmund Husserl believed, that we would indeed be in a nasty position, if 
empirical science were the only kind of science possible. 
-- 
Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de