[gmx-users] RE: problem with result from g_rdf

van Bemmelen J.J.M.vanBemmelen at student.TUDelft.NL
Mon Jan 7 00:44:22 CET 2008

So how large is this "small factor" compared to the rdf values? And does
this factor remain exactly constant as a function of r?

I'm only guessing, but it could be due to a slight difference in the r
used by you and by g_rdf (or equivalently a difference in the location
of a bin relative to r). Perhaps you're using the r at the beginning or
end of each bin, whereas g_rdf uses the value of r at the middle of each
bin. Or the other way around. This should give you slightly different
values for the rdf.

And another thing: probably you're already doing this, but shouldn't you
also divide by other factors, such as the particle density and the bin

Hope it helps,

John wrote:
> Using g_dist I got the distance between the atom pair for which i need
rdf.  Made a histogram, using the default bin width used in gromacs.
Then divide by 4*Pi*r^2 to normalize (where r is the distance between
the pair). I expect my values to agree with that from g_rdf. While the
graphs are exactly alike, the values from g_rdf are greater by a small
> Have I missed out something in my calculation?
> I would appreciate any help.
> Regards
> John

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