[gmx-users] problem with "gmx rdf": It cannot find the center of mass of a reference group

[Sajjad Kavyani]

Dear experts,
Recently I ask a question entitled "RDF of a group around CNT axis" in the
mailing list in order to find proper command-line for it it turns out that
the "-xy" option can help
But I encounter an unusual problem therefore I decided to ask another
question

It turns out that the gmx rdf cannot find the com coordinate of the CNT (as
reference) because as I choose different command-lines with various
"-selrpos" arguments, all of the results gave me EXACTLY the SAME result
which all of them are wrong! Commands like:
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos res_com
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos res_cog
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos mol_com
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos mol_cog
(CNT group has been chosen for both groups is gmx rdf)

But when I manually placed a single particle in the COM of the cnt (in the
cgs.gro) and then select this single particle as reference group, the gmx
rdf resulted the desired value!


Could you please help me to manage the problem?
How to tell the gmx rdf in order to find com of cnt without manually
placing a single particle in the input file?