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

[David van der Spoel]

Peyman Yamin wrote:
> 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!
xmgrace -nxy sas.xvg

> 
> 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. 


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se