From: Rudra Banerjee (
Date: Thu Jul 31 2008 - 00:46:01 CDT

Dear Alex,
thanks for your attention. I have read the "RTF(V)M" before mailing. but didnt get the idea. As i already written, i loaded *.psf and *.dcd file and then was trying to select the selection 1 and selection 2.
I also tried with the page written by you where it is shown how to plot g(r). but using something like cku_wb.pdb, its obviously plotting the g(r) of initial frame. but could not find out which file will give me the g(r) after (or on the course of md) simulation is over.

expecting help!

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----- Original Message ----
From: Axel Kohlmeyer <>
To: Rudra Banerjee <>
Sent: Thursday, 31 July, 2008 1:01:55 AM
Subject: Re: vmd-l: g(r)
On Wed, 30 Jul 2008, Rudra Banerjee wrote:
RB> with the risk of being advised to "RTFM", may i request you to let 
you'll only get an "RTFVM". :)
RB> me know, how to plot g(r) of NAMD output using VMD?
RB> actually, what is expected in selection1 and selection 2?
those are atom selections. the syntax is the same as for 
representations. details are in the VMD manual (see above). 
RB> i loaded the psf and dcd file, but failed to find the correct input for selections.
well, it is _very_ difficult to give somebody a specific 
help if the only information is "it didn't work". as this
tempts people to answer... "it works for me". ;)
the best way to not being RTFMed (or worse) is to follow
guidelines like presented in:
RB> also, i ll be happy, if anybody tell me how to retrive g(r) from NAMD outout.
so _what_ g(r) do you want to compute? and what did you try?
Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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