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pair_charmm.html
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<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>pair_style lj/charmm/coul/charmm command
</H3>
<H3>pair_style lj/charmm/coul/charmm/implicit command
</H3>
<H3>pair_style lj/charmm/coul/long command
</H3>
<H3>pair_style lj/charmm/coul/long/opt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I> or <I>lj/charmm/coul/long/opt</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/charmm/coul/charmm</I> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
<I>lj/charmm/coul/charmm/implicit</I> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
<I>lj/charmm/coul/long</I> args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/charmm/coul/charmm 8.0 10.0
pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</PRE>
<PRE>pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</PRE>
<PRE>pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long/opt 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/charmm</I> styles compute LJ and Coulombic interactions with an
additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cuoff. It is a widely
used potential in the <A HREF = "http://www.scripps.edu/brooks">CHARMM</A> MD code.
See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field.
</P>
<CENTER><IMG SRC = "Eqs/pair_charmm.jpg">
</CENTER>
<P>Both the LJ and Coulombic terms require an inner and outer cutoff.
They can be the same for both formulas or different depending on
whether 2 or 4 arguments are used in the pair_style command. In each
case, the inner cutoff distance must be less than the outer cutoff.
It it typical to make the difference between the 2 cutoffs about 1.0
Angstrom.
</P>
<P>Style <I>lj/charmm/coul/charmm/implicit</I> computes the same formulas as
style <I>lj/charmm/coul/charmm</I> except that an additional 1/r term is
included in the Coulombic formula. The Coulombic energy thus varies
as 1/r^2. This is effectively a distance-dependent dielectric term
which is a simple model for an implicit solvent with additional
screening. It is designed for use in a simulation of an unsolvated
biomolecule (no explicit water molecules).
</P>
<P>Style <I>lj/charmm/coul/long</I> computes the same formulas as style
<I>lj/charmm/coul/charmm</I> except that an additional damping factor is
applied to the Coulombic term, as in the discussion for pair style
<I>lj/cut/coul/long</I>. Only one Coulombic cutoff is specified for
<I>lj/charmm/coul/long</I>; if only 2 arguments are used in the pair_style
command, then the outer LJ cutoff is used as the single Coulombic
cutoff.
</P>
<P>Style <I>lj/charmm/coul/long/opt</I> is an optimized version of style
<I>lj/charmm/coul/long</I> that should give identical answers. Depending
on system size and the processor you are running on, it may be 5-25%
faster (for the pairwise portion of the run time).
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>epsilon_14 (energy units)
<LI>sigma_14 (distance units)
</UL>
<P>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
</P>
<P>The latter 2 coefficients are optional. If they are specified, they
are used in the LJ formula between 2 atoms of these types which are
also first and fourth atoms in any dihedral. No cutoffs are specified
because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, and rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
and sigma_14 coefficients for all of the lj/charmm pair styles can be
mixed. They are always mixed with the value <I>arithmetic</I>. See the
"pair_modify" command for details.
</P>
<P>None of the lj/charmm pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones
portion of the pair interaction is smoothed to 0.0 at the cutoff.
</P>
<P>The <I>lj/charmm/coul/long</I> and <I>lj/charmm/coul/long/opt</I> pair styles
support the <A HREF = "pair_modify.html">pair_modify</A> table option since they can
tabulate the short-range portion of the long-range Coulombic
interaction.
</P>
<P>None of the lj/charmm pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
corrections to energy and pressure, since the Lennard-Jones portion of
the pair interaction is smoothed to 0.0 at the cutoff.
</P>
<P>All of the lj/charmm pair styles can calculate per-atom energy and
stress, as used by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>,
<A HREF = "compute_stress_atom.html">compute stress/atom</A>, and <A HREF = "dump.html">dump
custom</A> commands.
</P>
<P>All of the lj/charmm pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>The lj/charmm/coul/long pair style supports the use of the <I>inner</I>,
<I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A>
command, meaning the pairwise forces can be partitioned by distance at
different levels of the rRESPA hierarchy. The other styles only
support the <I>pair</I> keyword of run_style respa. See the
<A HREF = "run_style.html">run_style</A> command for details.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I>
styles are part of the "molecule" package. The <I>lj/charmm/coul/long</I>
style is part of the "kspace" package. The <I>lj/charmm/coul/long/opt</I>
style is part of the "opt" package and also requires the "kspace"
package. They are only enabled if LAMMPS was built with those
package(s) (molecule and kspace are by default). See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>On some 64-bit machines, compiling with -O3 appears to break the
Coulombic tabling option used by the <I>lj/charmm/coul/long</I> style. See
the "Additional build tips" section of the Making LAMMPS documentation
pages for workarounds on this issue.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
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