Re: vmd-l: protein-water RDF

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
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,
Ajasja

On Mon, Jun 27, 2011 at 10:29, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>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<http://www.ks.uiuc.edu/Research/vmd/current/ug/node135.html>)
> 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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