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>special_bonds command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>special_bonds keyword values ...
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</PRE>
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<UL><LI>one or more keyword/value pairs may be appended
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<LI>keyword = <I>amber</I> or <I>charmm</I> or <I>fene</I> or <I>lj/coul</I> or <I>lj</I> or <I>coul</I> or <I>dihedral</I> or <I>extra</I>
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<PRE> <I>amber</I> values = none
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<I>charmm</I> values = none
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<I>fene</I> values = none
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<I>lj/coul</I> values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
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<I>lj</I> values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
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<I>coul</I> values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
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<I>dihedral</I> value = <I>yes</I> or <I>no</I>
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<I>extra</I> value = N
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N = number of extra 1-2,1-3,1-4 interactions to save space for
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</PRE>
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</UL>
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<P>Examples:
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</P>
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<PRE>special_bonds amber
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special_bonds charmm
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special_bonds fene dihedral no
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special_bonds lj/coul 0.0 0.0 0.5 dihedral yes
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special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
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special_bonds lj/coul 0 1 1 extra 2
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Set weighting coefficients for pairwise energy and force contributions
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from atom pairs that are also bonded to each other directly or
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indirectly. For Lennard-Jones (LJ) and Coulombic pairwise
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interactions, these coefficients come in sets of three. The 1st
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coefficient is the weighting factor on 1-2 atom pairs, which are those
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directly bonded to each other. The 2nd coefficient is the weighting
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factor on 1-3 atom pairs which are those separated by 2 bonds
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(e.g. the two H atoms in a water molecule). The 3rd coefficient is
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the weighting factor on 1-4 atom pairs which are those separated by 3
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bonds (e.g. the 1st and 4th atoms in a dihedral interaction). Thus if
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the 1-2 coefficient is set to 0.0, then the pairwise interaction is
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effectively turned off for all pairs of atoms bonded to each other.
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</P>
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<P>IMPORTANT NOTE: For purposes of computing weighted pairwise
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interactions, 1-3 and 1-4 interactions are not defined from the list
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of angles or dihedrals used by the simulation. Rather, they are
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inferred topologically from the set of bonds defined when the
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simulation is defined from a data or restart file (see
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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). Thus the set of 1-2,1-3,1-4 interactions that the weights
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apply to is the same whether angle and dihedral potentials are
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computed or not, and remains the same even if bonds are constrained,
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or turned off, or removed during a simulation.
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</P>
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<P>The two exceptions to this rule are (a) if the <I>dihedral</I> keyword is
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set to <I>yes</I> (see below), or (b) if the
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<A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I>
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option that recomputes the 1-2,1-3,1-4 topologies after bonds are
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deleted; see the <A HREF = "delete_bonds.html">delete_bonds</A> command for more
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details.
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</P>
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<P>The <I>amber</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
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interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
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is the default for a commonly used version of the AMBER force field,
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where the last value is really 5/6.
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</P>
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<P>The <I>charmm</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
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LJ and Coulombic interactions, which is the default for a commonly
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used version of the CHARMM force field. Note that in pair styles
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<I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/long</I> the 1-4 coefficients
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are defined explicitly, and these pairwise contributions are computed
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as part of the charmm dihedral style - see the
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<A HREF = "pair_coeff.html">pair_coeff</A> and <A HREF = "dihedral_style.html">dihedral_style</A>
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commands for more information.
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</P>
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<P>The <I>fene</I> keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
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LJ and Coulombic interactions, which is consistent with a
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coarse-grained polymer model with <A HREF = "bond_fene.html">FENE bonds</A>.
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</P>
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<P>The <I>lj/coul</I>, <I>lj</I>, and <I>coul</I> keywords allow the 3 coefficients to
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be set explicitly. The <I>lj/coul</I> keyword sets both the LJ and
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Coulombic coefficients to the same 3 values. The <I>lj</I> and <I>coul</I>
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keywords only set either the LJ or Coulombic coefficients. Use both
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of them if you wish to set the LJ coefficients to different values
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than the Coulombic coefficients.
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</P>
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<P>The <I>dihedral</I> keyword allows the 1-4 weighting factor to be ignored
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for individual atom pairs if they are not listed as the first and last
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atoms in any dihedral defined in the simulation. For example, imagine
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the 1-4 weighting factor is set to 0.5 and you have a linear molecule
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with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
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defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
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dihedral, then the pairwise interaction between atoms 1 and 4 will
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always be weighted by 0.5, but different force fields use different
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rules for weighting the pairwise interaction between atoms 2 and 5.
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If the <I>dihedral</I> keyword is specified as <I>yes</I>, then the pairwise
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interaction between atoms 2 and 5 will be unaffected (full weighting
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of 1.0). If the <I>dihedral</I> keyword is specified as <I>no</I> which is the
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default, then the 2,5 interaction will also be weighted by 0.5.
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</P>
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<P>The <I>extra</I> keyword is used when additional bonds will be created
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during a simulation run, e.g. by the <A HREF = "fix_bond_create.html">fix
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bond/create</A> command. A list of 1-2,1-3,1-4
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neighbors for each atom is calculated and stored by LAMMPS. If new
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bonds are created, the list needs to grow. Using the <I>extra</I> keyword
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leaves empty space in the list for N additional bonds to be added. If
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you do not do this, you may get an error when bonds are added.
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</P>
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<P><B>Restrictions:</B> none
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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 = "delete_bonds.html">delete_bonds</A>, <A HREF = "fix_bond_create.html">fix bond/create</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
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dihedral = no, and extra = 0.
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</P>
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</HTML>
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