[gmx-users] g_vanhove output

[Berk Hess]

I think I coded this all correctly, but the last time I used it was years ago.

In 3D you could plot G(x), G1(y) and G(z), which are equal for an isotropic liquid.
-or plots g(r) which is 2 pi r^2 G(r)

Berk

From: cari at purdue.edu
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] g_vanhove output
Date: Tue, 4 Aug 2009 11:02:51 -0400

Thanks Berk.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 diffusioncoefficient 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 a mistake
Thanks again,Marcelo
PS: I did consider the spherical integration.

On Aug 4, 2009, at 10:41 AM, Berk Hess wrote:Hi,

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?

Berk

> 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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