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
