Re: [AMBER] radial distribution function results

From: Daniel Roe <>
Date: Mon, 16 Sep 2013 09:41:15 -0600


Since the 'radial' functionality is also in cpptraj, the manual entry
for 'radial' in ptraj was removed for AmberTools 13, so I will be
referring to the AmberTools 12 manual for ptraj 'radial' (pg. 520).

On Mon, Sep 16, 2013 at 3:25 AM, Vijay Manickam Achari
<> wrote:
> radial rdfReults.dat 0.1 10 :DDM.O22 :WAT.H1,H2

I'm not certain what 'DDM' represents, but assuming it is some sort of
solute I think you may have your masks in reverse order: it should be
'<solvent mask> <solute mask>'. The order of masks is important when
calculating the RDF (otherwise the normalization may not be what you

> Upon running this command
> I get three files with extension *.xmgr, where the file name contains names such as carnal, standard, volume. And each files contains three columns. of numbers.

>From the AmberTools 12 manual:
'Three files are currently produced, "root-filename_carnal.xmgr"
(which corresponds to a carnal style RDF),
"root-filename_standard.xmgr" (which uses the more traditional RDF
with a density input by the user) and "root-filename_volume.xmgr"
(which uses the more traditional RDF and the average volume of the

> I am not sure why there are three files and each file contains three columns of numbers. Which file I should use to extract the values as a result.
> Could anyone share some idea on this? It well be great if I could get some explanation on this.

The 3 columns correspond to the coordinates of the left side of the
histogram bin, the normalized RDF, and the cumulative sum of the
averaged (but not normalized) bin values respectively. The
"root-filename_carnal.xmgr" file is provided mostly for
backwards-compatibility; you probably want to use the
"root-filename_standard.xmgr" or "root-filename_volume.xmgr" file. In
the "standard" file the RDF is normalized by a given density (or if
not specified 0.033456 mol/Ang^3, which corresponds to 1.0 g/mL). In
the "volume" file the average volume of the system is used for
normalization instead.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Sep 16 2013 - 09:00:03 PDT
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