[gmx-users] Question regarding g_rdf

[rainy908 at yahoo.com]

Hello,

I am fairly new to using Gromacs and am writing to seek clarification on the
g_rdf module.

In the manual, it states that "g_rdf calculates radial distribution
functions in different ways. The normal method is around a (set of)
particle(s), the other method is around the center of mass of a set of
particles."

Suppose a protein is solvated in a cubic water box.  If I interpret this
correctly, the former method only produces RDF values at a distance *outside
* of (or around) the protein.  The latter method produces RDF values within
the protein (distance from its center-of-mass).

I ask this because I am unsure how to utilize the -com flag:

$gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o
rdf_protein.xvg  (first method?)

$gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o
rdf_protein.xvg -com  (second method?)

Any helpful insights are most welcome.

Regards,
Lily
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