Dear all,
I calculated the radial distribution functions, g(r), of the solvent
(water TIP3P) with respect to
every atom of each residue of my peptide (from 0.0 Angs up to 6.0
Angs), with the following
command:
radial "name" 0.1 6.00 :WAT :"res"
For all the residues, g(r) plateaus from 0.0 Angs up to ~1.5 Angs and
then it starts increasing
and continues with a sort of oscillatory behaviour.
What I can not understand is why for few residues the value of the
g(r) initial plateau is
not zero but higher (for instance ~0.13 or ~0.2).
I would expect that every initial plateaus is at zero, as atoms have
finite dimensions.
Any clarification / suggestion would be really appreciated.
All the best,
--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 15 2011 - 05:30:05 PDT
