Re: [AMBER] Syntax Confusion on Radial Command

From: Thomas Cheatham <>
Date: Sun, 8 Mar 2015 16:29:37 -0600 (MDT)

> 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
> 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).

Yes, you are calculate the RDF of water oxygens around .C1 out to 12
Angstroms at bin intervals of 0.2 Angstroms.

> 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.

Yes, the "shape" should effectively be identical since likely your small
organic molecule is using the same (or similar) atom type(s) for all the
non-aromatic carbon atoms. What will influence the position of the first
peak is the non-bonded parameters of the atom.

The height of the peaks (and their integration) will depend somewhat on
the volume/shape of the solute. The bigger the solute and, depending on
the shape, may allow fewer waters into the first and second solvation
sphere around C1. This will reduce the peak heights and the integrated
number of waters... Let me know if you have further questions.


p.s. consider water W and solute C1 vs. C-C1-C

~6 waters in first shell


W C1 W


verse larger molecule

W C1 W

now only 4 waters in first shell...

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Received on Sun Mar 08 2015 - 15:30:03 PDT
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