[gmx-users] g_rdf gives odd results that don't add up?
thanksforallthefish at hotmail.com
Tue Mar 2 02:55:01 CET 2004
I'm trying to analyse a small molecule using g_rdf, after running it through
1. First question - what exactly is calculated per bin? Because I guess that
is some density, but it doesn't seem to correlate with either molecular
weight, molecular weight per unit volume, or number of atoms.
2. When I look at the resulting ".xvg" files, I sum them up in Microsoft
Excel and find that the difference in totals is about 33% higher if the
"-com" (centre of mass) option is turned on, than if it is left as the
Also I have observed that the density (at certain points) is higher if only
a certain subset of heavy atoms is included in the calculation, than if all
atoms in the structure are included. (This is while the "-com" option is
Any advice on how to make sense of these plots, or other options that I
would need to improve the data?
Thanks in advance
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