[gmx-users] g_rdf gives odd results that don't add up?

[Ben Roberts]

Hello All,

I'm trying to analyse a small molecule using g_rdf, after running it through 
a simulation.

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 
default (off).
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 
turned on.)

Any advice on how to make sense of these plots, or other options that I 
would need to improve the data?

Thanks in advance

Ben Roberts

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