[gmx-users] Questions about r_rdf in gromacs.4.6

[Chuipeng Kong]

Dear all,

I want to ask a question about g_rdf in gromacs.
For example, I have set up two groups, namely, A1 20 atoms, B1 20 atoms.
then I use the g_rdf commend:
g_rdf -f XXX.trr -s XXX.tpr -n XXX.ndx -o
then I selected two groups:
A1
B1
then I got the output rdf.xvg.

My question is: what am I computing?
My understanding is that I have collect distances between each pair
atoms from A1 and B1, and then
couple the result with radial distribution functions
Alternatively, I got rdf(A1_1 to B1), rdf(A1_2 to B1)... rdf (A1_20 to
B1). and Then sum up all the rdfs.

which is correct?

Thanks for your answer!

Chuipeng