[gmx-users] Normalization in g_rdf

Ondrej Marsalek ondrej.marsalek at gmail.com
Tue Nov 24 01:27:27 CET 2009

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?

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?

If these should work better than they do for me, I will of course
check my simulations again. I would just like to check first if this
is to be expected.


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