VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Apr 07 2008 - 15:32:29 CDT

On Mon, 7 Apr 2008, Raul Araya wrote:

RA> Dear VMD users:

dear raul,

RA> Im triying to calculate som RDFs from my simulation but there are at least
RA> two things I cannot understand.
RA>
RA> First: In the help web page for this plugin says that the file you save when
RA> one chooses to save a file of the calculated RDF
RA> should have four columns, but the files I have saved have only 3 of them,
RA> namely, r, g(r), and the integral numbers, but the raw histogram averaged
RA> over the number of frames, does not appear.

good point. this is an error in the documentation. the g(r) plugin is
a simple frontend for "measure gofr", so if you want something beyond
what the GUI offers, you'll have to run "measure gofr" directly from
the vmd console.

RA> Second: Should I divide the resulting RDFs by the number of frames in my
RA> trayectory?

no. this is already done in measure gofr.
please note, that for non-periodic or non-homogeneous systems,
the normalization depends on factors that go beyond what VMD
can derive from the available data, so we make some rather
arbitrary assumptions.

cheers,
  axel.

RA>
RA> Please help
RA>
RA> Raśl Araya Secchi B.Sc Molecular Biotechnology.
RA> Molecular Biotechnology Engineer.
RA> Centre for Bioinformatics CBUC, Faculty of Biological Sciences,
RA> P. Universidad Catolica de Chile
RA> Portugal # 49 ? ZIP 6513492 Santiago ?
RA> Chile Phone: + 56 2 6862269; http://www.cbuc.cl
RA> 

-- 
=======================================================================
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.