spoel at xray.bmc.uu.se
Fri Oct 24 22:45:01 CEST 2003
On Fri, 2003-10-24 at 21:57, Ilya Chorny wrote:
> 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?
I don't think it's the probe (but check it by all means).
Not sure about g_sorient, I only used it once. You definitely
should have only one angle for one configuration, but are you sure it
isn't xmgrace giving you a triangle? Look at the file.
> 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
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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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