Good afternoon,
I am having some confusion with the syntax of the "radial" command in
cpptraj. I have consulted the manual, played around with it on my own,
and *believe* I have the syntax worked out. However, given that I have
already fooled myself once in thinking I had the right syntax, I wish to
confirm explicitly.
radial rdf 0.2 12.0 :WAT.O :MOL.C1
[command] [output file name] [ bin size] [ max evaluated r value]
[solvent atom] [solute atom]
where
:WAT.O indicates the oxygen atom of ALL water molecules in the
simulation (since I did not specify a numeric string after this) [ this
is the point on which I seek clarification most]
:MOL.C1 indicates that the first carbon atom of all particles named
"MOL" (in my case, only one).
I infer that, as a matter of playing around with different small organic
molecules, that the rdf of a non-aromatic carbon atom in water is pretty
much the same, independent of the rest of the molecule.
Thank you for your time in reading this.
--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Sun Mar 08 2015 - 15:00:04 PDT
