VMD-L Mailing List
From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Thu Jul 31 2008 - 00:46:01 CDT
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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!
-- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html ----- Original Message ---- From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> To: Rudra Banerjee <bnrj.rudra_at_yahoo.com> Cc: vmd-l_at_ks.uiuc.edu 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: http://www.catb.org/~esr/faqs/smart-questions.html 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? cheers, axel. RB> RB> RB> -- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu 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 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
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