[gmx-users] RDF

mah maz mahmaz71 at gmail.com
Mon May 18 08:55:42 CEST 2015

Hi Justin
The fact is I want to calculate water density in the system. If I select
group1: oxygen and group2: oxygen, g_rdf command gives me very large
numbers. Is it the number of atoms that should be changed to g/cm3?
Besides, what does it calculate, each O is a reference atom during
Thanks a lot!

On Sun, May 17, 2015 at 2:17 PM, mah maz <mahmaz71 at gmail.com> wrote:

> Dear all,
> I want to calculate the radial distribution function of water molecules in
> my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which
> is not logical I suppose. Is it meaningful if I separate oxygen and
> hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is
> reference atom necessary to get RDF?
> Thanks!

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