[gmx-users] g_sas

David spoel at xray.bmc.uu.se
Fri Oct 24 21:43:01 CEST 2003

On Fri, 2003-10-24 at 01:51, Ilya Chorny wrote:
> Hello
> I ran the g_sas that came with the gromacs installation and I downloaded
> the most recent CVS version. I get completely different results. The
> original gives me more accurate results based on purely geometric
> arguments. The problem I have with the original version is that it gives
> me the same SAS per argon atom for an individual argon atom as compared
> with a string of argon atoms(i.e  A vs AAAAAA). Since water can't get in
> between the argon atoms I would expect a smaller SAS/Atom with the
> string. Am I doing something wrong?

It depends on the distance between the atoms and the size of the probe.
If you do it systematically by varying the distance between two atoms,
what do you get? If the distance is zero it should be the same as for
one atom, is it large it should be twice that...

(I'm pretty sure we fixed this one, and I also did comparison with
another program msms)

> Ilya
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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