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<div class="section" id="special-bonds-command">
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<span id="index-0"></span><h1>special_bonds command<a class="headerlink" href="#special-bonds-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>special_bonds keyword values ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>one or more keyword/value pairs may be appended</li>
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<li>keyword = <em>amber</em> or <em>charmm</em> or <em>dreiding</em> or <em>fene</em> or <em>lj/coul</em> or <em>lj</em> or <em>coul</em> or <em>angle</em> or <em>dihedral</em> or <em>extra</em></li>
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</ul>
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<pre class="literal-block">
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<em>amber</em> values = none
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<em>charmm</em> values = none
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<em>dreiding</em> values = none
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<em>fene</em> values = none
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<em>lj/coul</em> 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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<em>lj</em> 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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<em>coul</em> 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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<em>angle</em> value = <em>yes</em> or <em>no</em>
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<em>dihedral</em> value = <em>yes</em> or <em>no</em>
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<em>extra</em> 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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<p>Examples:</p>
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<div class="highlight-python"><div class="highlight"><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 angle yes 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></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Set weighting coefficients for pairwise energy and force contributions
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between pairs of atoms that are also permanently bonded to each other,
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either directly or via one or two intermediate bonds. These weighting
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factors are used by nearly all <a class="reference internal" href="pair_style.html"><em>pair styles</em></a> in LAMMPS
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that compute simple pairwise interactions. Permanent bonds between
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atoms are specified by defining the bond topology in the data file
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read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command. Typically a
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<a class="reference internal" href="bond_style.html"><em>bond_style</em></a> command is also used to define a bond
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potential. The rationale for using these weighting factors is that
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the interaction between a pair of bonded atoms is all (or mostly)
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specified by the bond, angle, dihedral potentials, and thus the
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non-bonded Lennard-Jones or Coulombic interaction between the pair of
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atoms should be excluded (or reduced by a weighting factor).</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">These weighting factors are NOT used by <a class="reference internal" href="pair_style.html"><em>pair styles</em></a> that compute many-body interactions, since the
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“bonds” that result from such interactions are not permanent, but are
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created and broken dynamically as atom conformations change. Examples
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of pair styles in this category are EAM, MEAM, Stillinger-Weber,
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Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
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sense to define permanent bonds between atoms that interact via these
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potentials, though such bonds may exist elsewhere in your system,
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e.g. when using the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> command.
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Thus LAMMPS ignores special_bonds settings when manybody potentials
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are calculated.</p>
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</div>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Unlike some commands in LAMMPS, you cannot use this command
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multiple times in an incremental fashion: e.g. to first set the LJ
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settings and then the Coulombic ones. Each time you use this command
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it sets all the coefficients to default values and only overrides the
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one you specify, so you should set all the options you need each time
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you use it. See more details at the bottom of this page.</p>
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</div>
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<p>The Coulomb factors are applied to any Coulomb (charge interaction)
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term that the potential calculates. The LJ factors are applied to the
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remaining terms that the potential calculates, whether they represent
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LJ interactions or not. The weighting factors are a scaling
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pre-factor on the energy and force between the pair of atoms. A value
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of 1.0 means include the full interaction; a value of 0.0 means
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exclude it completely.</p>
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<p>The 1st of the 3 coefficients (LJ or Coulombic) is the weighting
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factor on 1-2 atom pairs, which are pairs of atoms directly bonded to
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each other. The 2nd coefficient is the weighting factor on 1-3 atom
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pairs which are those separated by 2 bonds (e.g. the two H atoms in a
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water molecule). The 3rd coefficient is the weighting factor on 1-4
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atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th
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atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
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to 0.0, then the pairwise interaction is effectively turned off for
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all pairs of atoms bonded to each other. If it is set to 1.0, then
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that interaction will be at full strength.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">For purposes of computing weighted pairwise interactions, 1-3
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and 1-4 interactions are not defined from the list of angles or
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dihedrals used by the simulation. Rather, they are inferred
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topologically from the set of bonds specified when the simulation is
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defined from a data or restart file (see <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
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<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands). Thus the set of
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1-2,1-3,1-4 interactions that the weights apply to is the same whether
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angle and dihedral potentials are computed or not, and remains the
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same even if bonds are constrained, or turned off, or removed during a
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simulation.</p>
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</div>
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<p>The two exceptions to this rule are (a) if the <em>angle</em> or <em>dihedral</em>
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keywords are set to <em>yes</em> (see below), or (b) if the
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<a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a> command is used with the <em>special</em>
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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 class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a> command for more
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details.</p>
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<p>The <em>amber</em> 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. See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a> for a
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description of the AMBER force field.</p>
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<p>The <em>charmm</em> 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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<em>lj/charmm/coul/charmm</em> and <em>lj/charmm/coul/long</em> 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 class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> and <a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a>
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commands for more information. See <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> for a
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description of the CHARMM force field.</p>
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<p>The <em>dreiding</em> keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
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LJ and Coulombic interactions, which is the default for the Dreiding
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force field, as discussed in <a class="reference internal" href="#mayo"><span>(Mayo)</span></a>.</p>
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<p>The <em>fene</em> 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 class="reference internal" href="bond_fene.html"><em>FENE bonds</em></a>. See
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<a class="reference internal" href="#kremer"><span>(Kremer)</span></a> for a description of FENE bonds.</p>
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<p>The <em>lj/coul</em>, <em>lj</em>, and <em>coul</em> keywords allow the 3 coefficients to
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be set explicitly. The <em>lj/coul</em> keyword sets both the LJ and
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Coulombic coefficients to the same 3 values. The <em>lj</em> and <em>coul</em>
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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.</p>
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<p>The <em>angle</em> keyword allows the 1-3 weighting factor to be ignored for
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individual atom pairs if they are not listed as the first and last
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atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in
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any dihedral defined in the simulation. For example, imagine the 1-3
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weighting factor is set to 0.5 and you have a linear molecule with 4
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atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3
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as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a
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dihedral, then the pairwise interaction between atoms 1 and 3 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 4.
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If the <em>angle</em> keyword is specified as <em>yes</em>, then the pairwise
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interaction between atoms 2 and 4 will be unaffected (full weighting
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of 1.0). If the <em>angle</em> keyword is specified as <em>no</em> which is the
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default, then the 2,4 interaction will also be weighted by 0.5.</p>
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<p>The <em>dihedral</em> 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 <em>dihedral</em> keyword is specified as <em>yes</em>, 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 <em>dihedral</em> keyword is specified as <em>no</em> which is the
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default, then the 2,5 interaction will also be weighted by 0.5.</p>
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<p>The <em>extra</em> keyword can be used when additional bonds will be created
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during a simulation run, e.g. by the <a class="reference internal" href="fix_bond_create.html"><em>fix bond/create</em></a> command. It can also be used if
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molecules will be added to the system, e.g. via the <a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, or <a class="reference internal" href="fix_pour.html"><em>fix pour</em></a> commands, which
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will have atoms with more special neighbors than any atom in the
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current system has.</p>
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<hr class="docutils" />
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">LAMMPS stores and maintains a data structure with a list of the
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1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
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the system). If new bonds are created (or molecules added containing
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atoms with more special neighbors), the size of this list needs to
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grow. Note that adding a single bond always adds a new 1st neighbor
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but may also induce <em>many</em> new 2nd and 3rd neighbors, depending on the
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molecular topology of your system. Using the <em>extra</em> keyword leaves
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empty space in the list for this N additional 1st, 2nd, or 3rd
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neighbors to be added. If you do not do this, you may get an error
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when bonds (or molecules) are added.</p>
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</div>
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<hr class="docutils" />
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">If you reuse this command in an input script, you should set all
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the options you need each time. This command cannot be used a 2nd
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time incrementally, e.g. to add some extra storage locations via the
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<em>extra</em> keyword. E.g. these two commands:</p>
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</div>
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<p>special_bonds lj 0.0 1.0 1.0
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special_bonds coul 0.0 0.0 1.0</p>
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<p>are not the same as</p>
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<p>special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0</p>
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<p>In the first case you end up with (after the 2nd command):</p>
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<p>LJ: 0.0 0.0 0.0
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Coul: coul 0.0 0.0 1.0</p>
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<p>because the LJ settings are reset to their default values
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each time the command is issued.</p>
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<p>Likewise</p>
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<div class="highlight-python"><div class="highlight"><pre>special_bonds amber
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special_bonds extra 2
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</pre></div>
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</div>
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<p>is not the same as this single command:</p>
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<div class="highlight-python"><div class="highlight"><pre>special_bonds amber extra 2
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</pre></div>
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</div>
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<p>since in the former case, the 2nd command will reset all the LJ and
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Coulombic weights to 0.0 (the default).</p>
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<p>One exception to this rule is the <em>extra</em> option itself. It is not
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reset to its default value of 0 each time the special_bonds command is
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invoked. This is because it can also be set by the
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<a class="reference internal" href="read_data.html"><em>read_data</em></a> and <a class="reference internal" href="create_box.html"><em>create_box</em></a> commands,
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so this command will not override those settings unless you explicitly
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use <em>extra</em> as an option.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<blockquote>
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<div>none</div></blockquote>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a>, <a class="reference internal" href="fix_bond_create.html"><em>fix bond/create</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0,
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angle = no, dihedral = no, and extra = 0.</p>
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<hr class="docutils" />
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<p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
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Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
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