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

[Sajjad Kavyani]

Finally I managed to find the exact syntax for the rdf calculation by
adding " -ref 'com of group g1'  " at the end of the command-line:
gmx rdf -f cgs.gro   -s cgs.tpr   -o rdf.xvg  -xy  -ref 'com of group g1'

On Thu, Jun 8, 2017 at 12:56 AM, Sajjad Kavyani <kavyani.sajjad at gmail.com>
wrote:

> 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?
>