Calculation of RDF of a group indexed

User discussions
1

GROMACS version: 2021
GROMACS modification: No

Dear gromacs users,

I have questions about calculating the rdf of indexed group by myself. My system consists of molecule A having several ring group and some cations. I made index of each ring merging it in one group.

Here’s my question. If I calculate RDF between center of mass of ring and center of mass of cations, does gromacs calculate the rdf in the manner that “center of mass of each ring and center of mass of each cation?”

Please give me advice. It would be my honor if I get any advice.

With regards

2

Hi,
to calculate the RDF from one reference set of position to one or more sets of positions using the center of mass of molecule you can set the option -selrpos and -seltype to mol_com (default is atom).
See more option here
https://manual.gromacs.org/current/onlinehelp/gmx-rdf.html

Best regards
Alessandra