[AMBER] Syntax Confusion on Radial Command

From: Robert Molt <rwmolt07.gmail.com>
Date: Sun, 08 Mar 2015 17:55:59 -0400

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]


: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.
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
AMBER mailing list
Received on Sun Mar 08 2015 - 15:00:04 PDT
Custom Search