[gmx-users] Normalization in g_rdf
gmx3 at hotmail.com
Tue Nov 24 16:12:27 CET 2009
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.
> Date: Tue, 24 Nov 2009 13:23:30 +0100
> Subject: Re: [gmx-users] Normalization in g_rdf
> From: ondrej.marsalek at gmail.com
> To: gmx-users at gromacs.org
> On Tue, Nov 24, 2009 at 13:01, Omer Markovitch <omermar at gmail.com> wrote:
> > On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek <ondrej.marsalek at gmail.com>
> > wrote:
> >> Dear all,
> >> I would like to understand better the way g_rdf performs
> >> normalization. I have two unexpected results:
> >> 1) In a simple simulation of atomic ions in water in a cubic box, I
> >> get RDFs that clearly reach a constant value at large enough
> >> distances, but that value is somewhat lower than one. The simulation
> >> is NpT, could that be a problem for the normalization?
> > g(r) should fluctuate around 1 at large distances, say 9 Angstroms for pure
> > water.
> Indeed. However, see also Berk's remark. It seems to match very well
> for my system.
> >> 2) In a simulation in a dodecahedron, I get an unexpected decrease in
> >> the RDF at larger distances (for free ions in solution). Is there some
> >> know problem with normalization in triclinic cells? Is the RDF perhaps
> >> not truncated "soon" enough?
> > Try calculating it for much larger distances, if you have PBC this should
> > not be a problem even with the current docecahedron.
> Maybe I am missing something, but the range that g_rdf considers is
> hardwired - half the smallest box length with PBC, 3x the largest one
> without PBC. Is there a way to include contributions from multiple
> images of the unit cell?
> BTW, if g_rdf really only considers the box edge lengths and
> disregards angles, it would make sense that normalization is broken in
> general cells at larger distances, no?
> > --Omer.
> > --
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