[gmx-users] Normalization in g_rdf

Berk Hess gmx3 at hotmail.com
Tue Nov 24 17:39:01 CET 2009


Sure g_rdf takes care of pressure coupling, but the cut-off of the rdf plot is set from the initial frame.
So if your volume fluctuates a lot, you might have incorrect normalization very close to the cut-off.
But in "normal" liquid simulations the box length will never change more than 1%.


> Date: Tue, 24 Nov 2009 17:12:44 +0100
> Subject: Re: [gmx-users] Normalization in g_rdf
> From: ondrej.marsalek at gmail.com
> To: gmx-users at gromacs.org
> Hi again,
> I thought pressure coupling is handled by g_rdf. Looking at the code,
> it seems that the block starting with:
>     /* Must init pbc every step because of pressure coupling */
> takes care of that, so even with a relatively big volume change at the
> beginning, it should not be a problem. Is that not the case?
> Ondrej
> On Tue, Nov 24, 2009 at 16:12, Berk Hess <gmx3 at hotmail.com> wrote:
> > Hi,
> >
> > g_rdf limits the distance to half the minimum periodic image distance.
> > So the volume normalization is always simply  4 pi r^2.
> > It uses the starting unit-cell with a factor of 0.99.
> > So you would only see strange effects when the box length reduces
> > more than 1% due to pressure coupling.
> >
> > Berk
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