[AMBER] Fwd: radial distribution function between atoms of the two masks

From: Massimiliano Porrini <mozz76.gmail.com>
Date: Mon, 25 Feb 2013 21:54:20 +0100

Hi all,

Does anybody have any comment about my
below assumption?

Many thanks in advance,


Dr Massimiliano Porrini
Institut européen de chimie et biologie
2, rue Robert Escarpit
33607 Pessac, France
www.iecb.u-bordeaux.fr

E-mails: m.porrini.iecb.u-bordeaux.fr
             M.Porrini.ed.ac.uk
             mozz76.gmail.com
             maxp.iesl.forth.gr

Begin forwarded message:

> From: Massimiliano Porrini <m.porrini.iecb.u-bordeaux.fr>
> Date: 21 février 2013 15:12:24 UTC+01:00
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: radial distribution function between atoms of the two masks
>
> Dear all,
>
> I was surfing the Amber mailing list archives to find an answer to few doubts
> I had about the calculation of the radial distribution function (RDF)
> and I came across a
> very useful and explanatory email from Daniel Roe, the interesting excerpt
> of which I report below:
>
> *****************************************************************************
> Say I have a system composed of 2 residues, M
> (which has 6 atoms) and N (which has 3). If I do something like
> 'radial X 0.2 30.0 :N :M' I'm calculating these distances:
>
> N0->M0
> N0->M1
> N0->M2
> N0->M3
> N0->M4
> N0->M5
> N1->M0
> ...
> N2->M5
>
> I then normalize appropriately based on the number of atoms in each
> mask minus any overlap etc. When you do something like 'radial X 0.2
> 30.0 :M :N center1', now I'm calculating these distances:
>
> Center = {M0, M1, M2, M3, M4, M5}
> Center->N0
> Center->N1
> Center->N2
>
> This also gets normalized, but it is fundamentally a different
> calculation. Hopefully this makes things a little clearer.
> **********************************************************************************
>
> After calculating the above distances between all the possible
> pairs of atoms belonging to the two masks, what does ptraj/cpptraj do
> with them (apart from the normalization)?
> I am asking this question just because eventually we obtain only one
> RDF profile, that is a sort of measure of the density of *object_A*
> along the radial
> distance from *object_B* .
>
> My assumption is that the final profile is a kind of (weighted) mean of the
> above distances.
> Am I assuming well?
>
> Thanks a lot in advance and best wishes,
>
>
>
> --
> Dr Massimiliano Porrini
> Institut Européen de Chimie et Biologie (IECB)
> CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
> 2, rue Robert Escarpit
> 33607 Pessac Cedex
> FRANCE
>
> Tel : 33 (0)5 40 00 30 31
> Fax : 33 (0)5 40 00 22 00
> http://www.iecb.u-bordeaux.fr/
> Emails: m.porrini.iecb.u-bordeaux.fr
> M.Porrini.ed.ac.uk
> maxp.iesl.forth.gr
> mozz76.gmail.com
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Received on Mon Feb 25 2013 - 13:00:04 PST
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