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 Thu Feb 21 2013 - 06:30:02 PST
