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199 lines
8.3 KiB
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>
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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/cuda 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/charmm/implicit/cuda 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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<H3>pair_style lj/charmm/coul/long/cuda command
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</H3>
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<H3>pair_style lj/charmm/coul/long/gpu command
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</H3>
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<H3>pair_style lj/charmm/coul/long/opt command
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</H3>
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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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<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I>
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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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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 cutoff. It is a widely
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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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</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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<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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commands, or by mixing as described below:
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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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<HR>
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
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as the corresponding style without the suffix. They have been
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optimized to run faster, depending on your available hardware, as
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discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
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The accelerated styles take the same arguments and should produce the
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same results, except for round-off and precision issues.
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</P>
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<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
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packages respectively. They are only enabled if LAMMPS was built with
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those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info.
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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</P>
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<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
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instructions on how to use the accelerated styles effectively.
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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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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. The default mix value is <I>arithmetic</I> to coincide with the
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usual settings for the CHARMM force field. See the "pair_modify"
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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> style supports the
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<A HREF = "pair_modify.html">pair_modify</A> table option since it can tabulate the
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short-range portion of the long-range Coulombic interaction.
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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> 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 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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<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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<HR>
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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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style is part of the KSPACE package. They are only enabled if LAMMPS
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was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info. Note that
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the MOLECULE and KSPACE packages are installed by default.
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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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<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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</HTML>
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