[gmx-users] Normalization in g_rdf

Ondrej Marsalek ondrej.marsalek at gmail.com
Tue Nov 24 13:23:30 CET 2009

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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