[gmx-users] g_vanhove output

Berk Hess gmx3 at hotmail.com
Tue Aug 4 16:41:26 CEST 2009


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 consider
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, however
> 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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