From: Axel Kohlmeyer (
Date: Mon Jul 18 2011 - 09:40:28 CDT

On Mon, Jul 18, 2011 at 8:09 AM, Kartheek
<> wrote:
> Hi all,
> I am studying  Hydration Dynamics of nucleic acids, Trying to plot radial distribution function of oxygen atoms of phosphate back bone w.r.t oxygen atoms of water by using VMD plugins,but unable to succeed
> Steps which i have followed are
> 1.Loaded PSf file
> 2.Loaded DCD file
> 3.Analysis ---> Radial distribution function(RDF)
> under RDF there are two options shown
> Selection 1:
> selection 2:
> In selection 1, I have specified  as "oxygen atoms of phosphate backbone"
> In selection 2,I  have specified oxygen atoms of water
>  when i am executing this, it is showing some error in selection phrase,please tell me what is the correct phrase i have to use.

you have to use the "VMD atom selection language", i.e. the same keywords that
are used to select atoms for representations and with the atomselect command.
please look up the details in the VMD user's guide. it is also highly
that you first "practice" the selection on visualization representations, i.e.
load the data and show it with the default "Lines" and then create a
new selection
with one of the selection strings that you want (try "water") and show those as
VDW and you should see the selected atoms highlighted.

the exact phrase you need will depend on the details of your input data,
so you have to sort it out yourself.


> Any help from you will be highly appreciated.
> thanks in advance.
> From,
> Pitta kartheek.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.