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<HTML
><HEAD
><TITLE
></TITLE
><META
NAME="GENERATOR"
CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
REL="NEXT"
TITLE="Bibliography"
HREF="bibliography.html"></HEAD
><BODY
CLASS="ARTICLE"
BGCOLOR="#FFFFFF"
TEXT="#000000"
LINK="#0000FF"
VLINK="#840084"
ALINK="#0000FF"
><DIV
CLASS="ARTICLE"
><DIV
CLASS="SECT1"
><H1
CLASS="SECT1"
><A
NAME="JOELIB.DESCRIPTOR"
></A
>Descriptor</H1
><DIV
CLASS="SECT2"
><H2
CLASS="SECT2"
><A
NAME="JOELIB.DESCRIPTORS.RADIALDISTRIBUTIONFUNCTION"
></A
>Radial distribution function (RDF)</H2
><P
>The radial distribution function (RDF) [<A
HREF="bibliography.html#MSG99"
>msg99</A
>,<A
HREF="bibliography.html#WFZ04B"
>wfz04b</A
>] can be interpreted as the probability distribution of finding an atom in a spherical volume of
radius <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>r</B
></SPAN
>.
<DIV
CLASS="EQUATION"
><A
NAME="AEN14"
></A
><P
><B
>Equation 1. Radial distribution function</B
></P
><DIV
CLASS="MEDIAOBJECT"
><P
><IMG
SRC="formulas/rdf.gif"
ALIGN="CENTER"></P
></DIV
></DIV
>
where <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>r<SUB
>ij</SUB
></B
></SPAN
> is the geometrical distance between the atoms
<SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>i</B
></SPAN
> and atom <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>j</B
></SPAN
>, <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>w<SUB
>i</SUB
></B
></SPAN
>
and <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>w<SUB
>j</SUB
></B
></SPAN
> are the atom properties of the atoms <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>i</B
></SPAN
> and
<SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>j</B
></SPAN
>. <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>B</B
></SPAN
> is the smoothing parameter
(fuzziness of the distance <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>r<SUB
>ij</SUB
></B
></SPAN
>) for the interatomic distance and
<SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>f</B
></SPAN
> the scaling factor.</P
><P
>If <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>B</B
></SPAN
> aims to infinity the RDF code approximates to the autocorrelation function () and the fuzziness
of the distance <SPAN
CLASS="bold"
><B
CLASS="EMPHASIS"
>r<SUB
>ij</SUB
></B
></SPAN
> vanishes. So the RDF code can be treated as a generalized
autocorrelation function.</P
><P
>The RDF user parameters can be defined in the <TT
CLASS="FILENAME"
>joelib.properties</TT
>-file, otherwise the default parameters will be used:</P
><PRE
CLASS="PROGRAMLISTING"
>jcompchem.joelib.desc.types.RadialDistributionFunction.minSphericalVolume = 0.2
joelib.desc.types.RadialDistributionFunction.maxSphericalVolume = 10.0
joelib.desc.types.RadialDistributionFunction.sphericalVolumeResolution = 0.2
joelib.desc.types.RadialDistributionFunction.smoothingFactor = 25</PRE
><P
>Optional the RDF can be calculated with protonated molecules, but you must be sure that all available atom
properties are calculated with hydrogens also. Because this is not the standard, this option should be only used by developers.</P
></DIV
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