VMD-L Mailing List

From: syma (syma.khalid_at_bioch.ox.ac.uk)
Date: Tue Mar 27 2007 - 16:49:06 CDT

Axel,
Many thanks for your prompt help with this.

Best wishes,

-Syma

-----Original Message-----
From: Axel Kohlmeyer [mailto:akohlmey_at_cmm.chem.upenn.edu]
Sent: 27 March 2007 22:44
To: syma
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: rdf using gui

On Tue, 27 Mar 2007, syma wrote:

SK> Hi,
SK>
SK> Please can someone help.
SK>
SK> I am trying to use the RDF GUI in vmd 1.8.5 (windows and linux).
SK> I want to calculate the RDF of two types of lipids around another
species in
SK> my system. There are 119 lipid molecules of one type and 116 of the
other.
SK> Do I need to do some sort of normalisation before I can compare the
RDFs, or
SK> indeed is it possible to compare RDFs in this way?

the RDFs are normalized with respect to the total particle density of
the system cell (if given and PBC is activated). whether this is useful
for a comparison depends on your setup. as an alternative, you may
compare the number integrals, which are based on particle counts...

note that the code does not distinguish between atom types, it just
takes all atoms in a selection as one type and only handles double
counting between them (i.e. it doesn't event try to be smart. you
have to make sure that you feed it the right selections).

cheers,
   axel.

SK>
SK> Many thanks for your help,
SK>
SK> -Syma
SK>
SK> ***************************************************
SK>
SK> Dr Syma Khalid
SK> Department of Biochemistry,
SK> University of Oxford
SK> South Parks Road,
SK> Oxford
SK> OX1 3QU
SK> U.K.
SK>
SK>
SK>
SK> ***************************************************
SK>
SK> 

-- 
=======================================================================
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
=======================================================================
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