[gmx-users] Question about center of mass definition in RDF tool (gromacs 5.11)

Sergio Garay sergio.alberto.garay at gmail.com
Wed Jun 5 14:49:27 CEST 2019

Hi all

My name is Sergio Garay, and I've simulated a micelle formed by 30
molecules in water. Each of my molecules are made up of 5 residues and I
want to calculate the RDF of each residue around the micelle center of
mass. I've use rdf tool from gromacs_5.11 to do the calculation, but I'm
not sure if I've done the correct selection of the reference:

*-selrpos whole_mol_com* --> (and I select a group with all molecules as
it will select the com of all molecules as reference?

What about if I want to use the com of a group of particular atoms as
What it would be the correct option? Is this: "part_res_com"?

Thank you for your time


*Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs.
BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 -
Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54
(342) 4575-221 *

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