[gmx-users] radial distribution function

Qiao Baofu qiaobf at gmail.com
Wed Nov 22 13:39:45 CET 2006

To my knowledge, g_rdf calculate all the atoms of group A to all the atoms
of group B to get the gAB(r). g_rdf -com calculate the center of group A,
not the centers of the residues in group A to all the atoms of group B.

I upload a file based on gmx_rdf.c to calculate the centers of residues of
group A (and B) last month to the website of gromacs.

2006/11/22, Nguyen Hoang Phuong <phuong at theochem.uni-frankfurt.de>:
> 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
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Baofu Qiao
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