[gmx-users] RDF analysis with respect to center of mass of Protein

[Carlos Navarro Retamal]

Dear gromacs users,
In order to measure the interactions between a Protein with respect to a mixture solvent solution  (glycerol-water) i’m trying to measure the RDF between the protein with respect to the C and O atoms of Glycerol respectively.
By now i have measured g(r) between:

Protein - Glycerol
Protein Backbone - Glycerol
SideChain - Glycerol

but sadly, because i’m considering a huge amount of atoms of the Protein, the RDF graphic doesn’t look that good.
On that way i thought that maybe a better approximation will be to measure the RDF between the center of Mass of the protein with respect to the glycerol molecules, but i don’t know how to use make_ndx to create such kind of group.
Is there a way to do this? Or maybe you may think in a better idea.
Hope someone can help me.
Best regards,
Carlos  

--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl