2006-09-22 00:22:34 +08:00
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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>
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<HR>
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<H3>pair_style lj/charmm/coul/charmm command
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</H3>
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<H3>pair_style lj/charmm/coul/charmm/implicit command
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</H3>
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<H3>pair_style lj/charmm/coul/long command
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</H3>
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2007-02-10 05:40:32 +08:00
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<H3>pair_style lj/charmm/coul/long/opt command
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</H3>
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2006-09-22 00:22:34 +08:00
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style style args
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</PRE>
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2007-02-10 05:40:32 +08:00
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<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>
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2006-09-22 00:22:34 +08:00
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<LI>args = list of arguments for a particular style
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</UL>
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<PRE> <I>lj/charmm/coul/charmm</I> args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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<I>lj/charmm/coul/charmm/implicit</I> args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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<I>lj/charmm/coul/long</I> args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style lj/charmm/coul/charmm 8.0 10.0
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pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5
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</PRE>
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<PRE>pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
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pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5
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</PRE>
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<PRE>pair_style lj/charmm/coul/long 8.0 10.0
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2007-02-10 05:40:32 +08:00
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pair_style lj/charmm/coul/long/opt 8.0 10.0
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2006-09-22 00:22:34 +08:00
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pair_style lj/charmm/coul/long 8.0 10.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>lj/charmm</I> styles compute LJ and Coulombic interactions with an
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additional switching function S(r) that ramps the energy and force
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smoothly to zero between an inner and outer cuoff. It is a widely
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2006-09-28 03:12:31 +08:00
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used potential in the <A HREF = "http://www.scripps.edu/brooks">CHARMM</A> MD code.
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See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
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field.
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2006-09-22 00:22:34 +08:00
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</P>
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<CENTER><IMG SRC = "Eqs/pair_charmm.jpg">
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</CENTER>
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<P>Both the LJ and Coulombic terms require an inner and outer cutoff.
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They can be the same for both formulas or different depending on
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whether 2 or 4 arguments are used in the pair_style command. In each
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case, the inner cutoff distance must be less than the outer cutoff.
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It it typical to make the difference between the 2 cutoffs about 1.0
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Angstrom.
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</P>
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<P>Style <I>lj/charmm/coul/charmm/implicit</I> computes the same formulas as
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style <I>lj/charmm/coul/charmm</I> except that an additional 1/r term is
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included in the Coulombic formula. The Coulombic energy thus varies
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as 1/r^2. This is effectively a distance-dependent dielectric term
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which is a simple model for an implicit solvent with additional
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screening. It is designed for use in a simulation of an unsolvated
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biomolecule (no explicit water molecules).
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</P>
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<P>Style <I>lj/charmm/coul/long</I> computes the same formulas as style
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<I>lj/charmm/coul/charmm</I> except that an additional damping factor is
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applied to the Coulombic term, as in the discussion for pair style
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<I>lj/cut/coul/long</I>. Only one Coulombic cutoff is specified for
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<I>lj/charmm/coul/long</I>; if only 2 arguments are used in the pair_style
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command, then the outer LJ cutoff is used as the single Coulombic
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cutoff.
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</P>
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2007-02-10 05:40:32 +08:00
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<P>Style <I>lj/charmm/coul/long/opt</I> is an optimized version of style
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<I>lj/charmm/coul/long</I> that should give identical answers. Depending
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on system size and the processor you are running on, it may be 5-25%
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faster (for the pairwise portion of the run time).
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</P>
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2006-09-22 00:22:34 +08:00
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<P>The following coefficients must be defined for each pair of atoms
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types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
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above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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2007-06-25 22:36:36 +08:00
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commands, or by mixing as described below:
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2006-09-22 00:22:34 +08:00
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</P>
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<UL><LI>epsilon (energy units)
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<LI>sigma (distance units)
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<LI>epsilon_14 (energy units)
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<LI>sigma_14 (distance units)
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</UL>
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<P>Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.
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</P>
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<P>The latter 2 coefficients are optional. If they are specified, they
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are used in the LJ formula between 2 atoms of these types which are
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also first and fourth atoms in any dihedral. No cutoffs are specified
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because this CHARMM force field does not allow varying cutoffs for
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individual atom pairs; all pairs use the global cutoff(s) specified in
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the pair_style command.
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</P>
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2007-06-25 22:36:36 +08:00
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<HR>
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2007-10-04 08:21:14 +08:00
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<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
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restart, and rRESPA info</B>:
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2007-06-25 22:36:36 +08:00
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</P>
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<P>For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
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and sigma_14 coefficients for all of the lj/charmm pair styles can be
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mixed. They are always mixed with the value <I>arithmetic</I>. See the
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"pair_modify" command for details.
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</P>
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<P>None of the lj/charmm pair styles support the
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<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones
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portion of the pair interaction is smoothed to 0.0 at the cutoff.
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</P>
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<P>The <I>lj/charmm/coul/long</I> and <I>lj/charmm/coul/long/opt</I> pair styles
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support the <A HREF = "pair_modify.html">pair_modify</A> table option since they can
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tabulate the short-range portion of the long-range Coulombic
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interaction.
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2007-04-20 07:25:27 +08:00
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</P>
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2007-06-25 22:36:36 +08:00
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<P>None of the lj/charmm pair styles support the
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<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
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corrections to energy and pressure, since the Lennard-Jones portion of
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the pair interaction is smoothed to 0.0 at the cutoff.
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</P>
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<P>All of the lj/charmm pair styles can calculate per-atom energy and
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stress, as used by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>,
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<A HREF = "compute_stress_atom.html">compute stress/atom</A>, and <A HREF = "dump.html">dump
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custom</A> commands.
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</P>
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<P>All of the lj/charmm pair styles write their information to <A HREF = "restart.html">binary
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restart files</A>, so pair_style and pair_coeff commands do
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not need to be specified in an input script that reads a restart file.
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</P>
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2007-10-04 08:21:14 +08:00
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<P>The lj/charmm/coul/long pair style supports the use of the <I>inner</I>,
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<I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A>
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command, meaning the pairwise forces can be partitioned by distance at
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different levels of the rRESPA hierarchy. The other styles only
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support the <I>pair</I> keyword of run_style respa. See the
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<A HREF = "run_style.html">run_style</A> command for details.
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</P>
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2007-06-25 22:36:36 +08:00
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<HR>
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2006-09-22 00:22:34 +08:00
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<P><B>Restrictions:</B>
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</P>
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<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I>
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styles are part of the "molecule" package. The <I>lj/charmm/coul/long</I>
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2007-02-10 05:40:32 +08:00
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style is part of the "kspace" package. The <I>lj/charmm/coul/long/opt</I>
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style is part of the "opt" package and also requires the "kspace"
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package. They are only enabled if LAMMPS was built with those
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2007-06-25 22:36:36 +08:00
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package(s) (molecule and kspace are by default). See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>On some 64-bit machines, compiling with -O3 appears to break the
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Coulombic tabling option used by the <I>lj/charmm/coul/long</I> style. See
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the "Additional build tips" section of the Making LAMMPS documentation
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pages for workarounds on this issue.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>
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</P>
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<P><B>Default:</B> none
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</P>
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2006-09-28 03:12:31 +08:00
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<HR>
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<A NAME = "MacKerell"></A>
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<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
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Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
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</P>
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2006-09-22 00:22:34 +08:00
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</HTML>
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