Re: vmd-l: protein-water RDF

From: Ajasja Ljubetič (
Date: Mon Jun 27 2011 - 03:33:13 CDT

Sorry everybody for the wrong cross posting of the previous message to the
NAMD mailing list.
I meant to send it to the VMD mailing list...

Best regards,

On Mon, Jun 27, 2011 at 10:29, Ajasja Ljubetič <>wrote:

> Hi,
> 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 gofr<>)
> 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
> dir>\plugins\noarch\tcl\gofrgui1.2"
> 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.
> Regards,
> Ajasja

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