[gmx-users] radial distribution function

[Nguyen Hoang Phuong]

Hi All,

I would like to compute the radial distribution
function g(r) between solvent molecules and a group of
atoms of the solute. To this end, I define two groups
in the index.ndx file: one for solvent and one for a
peptide group. The index file looks like:

[ Pep ]
1
2
3
4
[ Sol]
10
11
12
...

My question is that how does gromacs compute
g(r)? Is r the distance between center of mass
of the group [ Pep ] and the center of mass of each
solvent molecule? Or gromacs computes g_i(r) between
each atom of the group [ Pep] with respect to solvent
molecules and then take average over all g_i(r) to get
g(r)?

Many thanks in advance,

Phuong