[gmx-users] g_vanhove output
cari at purdue.edu
Tue Aug 4 17:02:51 CEST 2009
I did look at the code, but it is not that easy to understand.
My conclusion comes from this:
for a diffusive regime, G(r) should be a gaussian function, with the
coefficient characterizing the width.
I did some tests, and I could match both curves (one from g_vanhove and
the other from the diff.coef) only if I multiply the output of
g_vanhove by r and normalizing again, which makes little sense to me.
It would be ok to output G(r) or r^2*G(r), but to output r*G(r) seems
PS: I did consider the spherical integration.
On Aug 4, 2009, at 10:41 AM, Berk Hess wrote:
> You can look at the code yourself :)
> I coded this and -or (which I assume you are talking about)
> is G with 1/nm as a unit.
> It gives the probability that a particle has moved a distance r.
> The 1/nm is the normalization to make the values bin-size independent.
> Might it be that the difference in interpretation comes from if you
> normalization of the volume of sphere-shells or not?
> > From: cari at purdue.edu
> > To: gmx-users at gromacs.org
> > Date: Tue, 4 Aug 2009 10:25:33 -0400
> > Subject: [gmx-users] g_vanhove output
> > Hi all,
> > I believe there is a mistake in g_vanhove in version 4.0.5
> > The 'xvg' output file labels the y axis as G, with nm^-1 as units.
> > From the units, I guessed that the output was actually r^2 G,
> > the initial slope is linear and not quadratic. After a few tries I
> > concluded that
> > the output is actually r*G, which is not something really useful.
> > I wonder if someone could look at the code and confirm this doubt in
> > one way or another.
> > Many thank,
> > Marcelo Carignano.
> > PS: I couldn't find this on the list, but it has been difficult to
> > access the
> > archives lately.
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