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

Carlos Navarro Retamal cnavarro at utalca.cl
Thu Sep 18 20:04:38 CEST 2014

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 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

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