Re: vmd-l: protein-water RDF

From: Ajasja Ljubetič (
Date: Mon Jun 27 2011 - 03:29:44 CDT


> Yeah I have done that. It shows all the atoms of protein. So does this mean
> that while calculating RDF between protein and water (oxygen), it considers
> distances of oxygens of water from each atom of protein? Or it takes the
> center of mass of protein ?

In the manual (for measure
it says that it calculates the RDF "for all pairs of atoms in the two
selections" so I guess it takes all the atoms of the protein.

Morevover, from where can I obtain the in-built tcl script for calculation
> of RDF that VMD uses?

The source for the plugin can be found under "<VMD install
It's a wrapper around VMD's measure gofr and measure rdf commands. But I'm
not sure if these two commands are implemented using TCL. Most probably they
are not.


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