[gmx-users] g_sas

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Fri Oct 24 21:58:00 CEST 2003

I agree. I have six argon atoms strung together at a distance of sigma
but the sas I get for one argon atom is 1/6th the sas for the six atoms.
Water should no be able to get inbetween the the argon atoms. Is it
becasue the default probe is to small?  David could you also take a look
at the first part of of g_sorient question?



On Fri, 2003-10-24 at 14:31, David wrote:
> 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

More information about the gromacs.org_gmx-users mailing list