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rLAMMPS lammps
compute_gyration_molecule.html
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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute gyration/molecule command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID gyration/molecule
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>gyration/molecule = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 molecule gyration/molecule
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the radius of gyration Rg of
individual molecules. The calculation includes all effects due to
atoms passing thru periodic boundaries.
</P>
<P>Rg is a measure of the size of a molecule, and is computed by this
formula
</P>
<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
</CENTER>
<P>where M is the total mass of the molecule and Rcm is the center-of-mass
position of the molecule.
</P>
<P>Rg for a particular molecule is only computed if one or more of its
atoms are in the specified group. Normally all atoms in the molecule
should be in the group, however this is not required. LAMMPS will
warn you if this is not the case. Only atoms in the group contribute
to the Rg calculation for the molecule.
</P>
<P>Let Nmolecules be the number of molecules for which Rg is calculated.
If not all molecules have atoms in the group, then the molecule with
the lowest ID is the first of the Nmolecules. The next lowest ID is
the second, etc, up to Nmolecules.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
"unwrapped" form, by using the image flags associated with each atom.
See the <A HREF = "dump.html">dump custom</A> command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global vector of Rg values with the number
of elements = Nmolecules. These values can be used by any command
that uses a global vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The vector values calculated by this compute are "intensive", meaning
it is independent of the number of atoms in the simulation.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><A HREF = "compute_gyration.html">compute gyration</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
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