ichorny at maxwell.compbio.ucsf.edu
Fri Oct 24 23:06:02 CEST 2003
If I make the distance zero I still get 6 times the sas of one argon.
very starnge. I checked it against msms and got very different results.
Its not xmgrace the xvg file has a distribution. Maybe I will try the
CVS version. Do you know of anyone who uses g_sorient?
On Fri, 2003-10-24 at 15:33, David wrote:
> 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.
> > Thanks
> > Ilya
> > 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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