On Wednesday 30 July 2008 12:58, David van der Spoel wrote:
> 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
Thanks David, but what about other question marks?!
What is hydrophilic area? is it the wetted or solvated or maybe area on which
the solvent molecules are with less than a distance apart from surface, or
something else? In Triton, the length of the part which is interacting in a
hydrophilic way is bigger actually, but I see a result of g_sas telling me that
hydrophobic area is ~50 times bigger!!
I use ffG43a1. Is it a strange behavior to calculate SAS from a UA
trajectory?
I mean is the CHx groups' H size taken intro account ?
> >
How is the DGsolv calculated by g_sas? and the areas ? which algorithm?
where is the code? reference?
> >
Is there any program with which one could calculate the volume enclosed
by SAS resulted from g_sas? Just if one used such and can trust any code
available anywhere??
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
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