forked from lijiext/lammps
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585 lines
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<div class="section" id="special-bonds-command">
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<span id="index-0"></span><h1>special_bonds command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<pre class="literal-block">
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special_bonds keyword values ...
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</pre>
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<ul>
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<li><p class="first">one or more keyword/value pairs may be appended</p>
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</li>
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<li><p class="first">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></p>
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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>
|
|
<em>dihedral</em> value = <em>yes</em> or <em>no</em>
|
|
<em>extra</em> value = N
|
|
N = number of extra 1-2,1-3,1-4 interactions to save space for
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
<p>Examples:</p>
|
|
<pre class="literal-block">
|
|
special_bonds amber
|
|
special_bonds charmm
|
|
special_bonds fene dihedral no
|
|
special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
|
|
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
|
|
special_bonds lj/coul 0 1 1 extra 2
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Set weighting coefficients for pairwise energy and force contributions
|
|
between pairs of atoms that are also permanently bonded to each other,
|
|
either directly or via one or two intermediate bonds. These weighting
|
|
factors are used by nearly all <a class="reference internal" href="pair_style.html"><span class="doc">pair styles</span></a> in LAMMPS
|
|
that compute simple pairwise interactions. Permanent bonds between
|
|
atoms are specified by defining the bond topology in the data file
|
|
read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. Typically a
|
|
<a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> command is also used to define a bond
|
|
potential. The rationale for using these weighting factors is that
|
|
the interaction between a pair of bonded atoms is all (or mostly)
|
|
specified by the bond, angle, dihedral potentials, and thus the
|
|
non-bonded Lennard-Jones or Coulombic interaction between the pair of
|
|
atoms should be excluded (or reduced by a weighting factor).</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">These weighting factors are NOT used by <a class="reference internal" href="pair_style.html"><span class="doc">pair styles</span></a> that compute many-body interactions, since the
|
|
“bonds” that result from such interactions are not permanent, but are
|
|
created and broken dynamically as atom conformations change. Examples
|
|
of pair styles in this category are EAM, MEAM, Stillinger-Weber,
|
|
Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
|
|
sense to define permanent bonds between atoms that interact via these
|
|
potentials, though such bonds may exist elsewhere in your system,
|
|
e.g. when using the <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid</span></a> command.
|
|
Thus LAMMPS ignores special_bonds settings when manybody potentials
|
|
are calculated.</p>
|
|
</div>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Unlike some commands in LAMMPS, you cannot use this command
|
|
multiple times in an incremental fashion: e.g. to first set the LJ
|
|
settings and then the Coulombic ones. Each time you use this command
|
|
it sets all the coefficients to default values and only overrides the
|
|
one you specify, so you should set all the options you need each time
|
|
you use it. See more details at the bottom of this page.</p>
|
|
</div>
|
|
<p>The Coulomb factors are applied to any Coulomb (charge interaction)
|
|
term that the potential calculates. The LJ factors are applied to the
|
|
remaining terms that the potential calculates, whether they represent
|
|
LJ interactions or not. The weighting factors are a scaling
|
|
pre-factor on the energy and force between the pair of atoms. A value
|
|
of 1.0 means include the full interaction; a value of 0.0 means
|
|
exclude it completely.</p>
|
|
<p>The 1st of the 3 coefficients (LJ or Coulombic) is the weighting
|
|
factor on 1-2 atom pairs, which are pairs of atoms directly bonded to
|
|
each other. The 2nd coefficient is the weighting factor on 1-3 atom
|
|
pairs which are those separated by 2 bonds (e.g. the two H atoms in a
|
|
water molecule). The 3rd coefficient is the weighting factor on 1-4
|
|
atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th
|
|
atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
|
|
to 0.0, then the pairwise interaction is effectively turned off for
|
|
all pairs of atoms bonded to each other. If it is set to 1.0, then
|
|
that interaction will be at full strength.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">For purposes of computing weighted pairwise interactions, 1-3
|
|
and 1-4 interactions are not defined from the list of angles or
|
|
dihedrals used by the simulation. Rather, they are inferred
|
|
topologically from the set of bonds specified when the simulation is
|
|
defined from a data or restart file (see <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or
|
|
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> commands). Thus the set of
|
|
1-2,1-3,1-4 interactions that the weights apply to is the same whether
|
|
angle and dihedral potentials are computed or not, and remains the
|
|
same even if bonds are constrained, or turned off, or removed during a
|
|
simulation.</p>
|
|
</div>
|
|
<p>The two exceptions to this rule are (a) if the <em>angle</em> or <em>dihedral</em>
|
|
keywords are set to <em>yes</em> (see below), or (b) if the
|
|
<a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command is used with the <em>special</em>
|
|
option that recomputes the 1-2,1-3,1-4 topologies after bonds are
|
|
deleted; see the <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command for more
|
|
details.</p>
|
|
<p>The <em>amber</em> keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
|
|
interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
|
|
is the default for a commonly used version of the AMBER force field,
|
|
where the last value is really 5/6. See <a class="reference internal" href="#cornell"><span class="std std-ref">(Cornell)</span></a> for a
|
|
description of the AMBER force field.</p>
|
|
<p>The <em>charmm</em> keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
|
|
LJ and Coulombic interactions, which is the default for a commonly
|
|
used version of the CHARMM force field. Note that in pair styles
|
|
<em>lj/charmm/coul/charmm</em> and <em>lj/charmm/coul/long</em> the 1-4 coefficients
|
|
are defined explicitly, and these pairwise contributions are computed
|
|
as part of the charmm dihedral style - see the
|
|
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> and <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a>
|
|
commands for more information. See <a class="reference internal" href="#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a
|
|
description of the CHARMM force field.</p>
|
|
<p>The <em>dreiding</em> keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
|
|
LJ and Coulombic interactions, which is the default for the Dreiding
|
|
force field, as discussed in <a class="reference internal" href="#mayo"><span class="std std-ref">(Mayo)</span></a>.</p>
|
|
<p>The <em>fene</em> keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
|
|
LJ and Coulombic interactions, which is consistent with a
|
|
coarse-grained polymer model with <a class="reference internal" href="bond_fene.html"><span class="doc">FENE bonds</span></a>. See
|
|
<a class="reference internal" href="#kremer"><span class="std std-ref">(Kremer)</span></a> for a description of FENE bonds.</p>
|
|
<p>The <em>lj/coul</em>, <em>lj</em>, and <em>coul</em> keywords allow the 3 coefficients to
|
|
be set explicitly. The <em>lj/coul</em> keyword sets both the LJ and
|
|
Coulombic coefficients to the same 3 values. The <em>lj</em> and <em>coul</em>
|
|
keywords only set either the LJ or Coulombic coefficients. Use both
|
|
of them if you wish to set the LJ coefficients to different values
|
|
than the Coulombic coefficients.</p>
|
|
<p>The <em>angle</em> keyword allows the 1-3 weighting factor to be ignored for
|
|
individual atom pairs if they are not listed as the first and last
|
|
atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in
|
|
any dihedral defined in the simulation. For example, imagine the 1-3
|
|
weighting factor is set to 0.5 and you have a linear molecule with 4
|
|
atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3
|
|
as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a
|
|
dihedral, then the pairwise interaction between atoms 1 and 3 will
|
|
always be weighted by 0.5, but different force fields use different
|
|
rules for weighting the pairwise interaction between atoms 2 and 4.
|
|
If the <em>angle</em> keyword is specified as <em>yes</em>, then the pairwise
|
|
interaction between atoms 2 and 4 will be unaffected (full weighting
|
|
of 1.0). If the <em>angle</em> keyword is specified as <em>no</em> which is the
|
|
default, then the 2,4 interaction will also be weighted by 0.5.</p>
|
|
<p>The <em>dihedral</em> keyword allows the 1-4 weighting factor to be ignored
|
|
for individual atom pairs if they are not listed as the first and last
|
|
atoms in any dihedral defined in the simulation. For example, imagine
|
|
the 1-4 weighting factor is set to 0.5 and you have a linear molecule
|
|
with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
|
|
defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
|
|
dihedral, then the pairwise interaction between atoms 1 and 4 will
|
|
always be weighted by 0.5, but different force fields use different
|
|
rules for weighting the pairwise interaction between atoms 2 and 5.
|
|
If the <em>dihedral</em> keyword is specified as <em>yes</em>, then the pairwise
|
|
interaction between atoms 2 and 5 will be unaffected (full weighting
|
|
of 1.0). If the <em>dihedral</em> keyword is specified as <em>no</em> which is the
|
|
default, then the 2,5 interaction will also be weighted by 0.5.</p>
|
|
<p>The <em>extra</em> keyword can be used when additional bonds will be created
|
|
during a simulation run, e.g. by the <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix bond/create</span></a> command. It can also be used if
|
|
molecules will be added to the system, e.g. via the <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>, or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a> commands, which
|
|
will have atoms with more special neighbors than any atom in the
|
|
current system has.</p>
|
|
<hr class="docutils" />
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">LAMMPS stores and maintains a data structure with a list of the
|
|
1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
|
|
the system). If new bonds are created (or molecules added containing
|
|
atoms with more special neighbors), the size of this list needs to
|
|
grow. Note that adding a single bond always adds a new 1st neighbor
|
|
but may also induce *many* new 2nd and 3rd neighbors, depending on the
|
|
molecular topology of your system. Using the <em>extra</em> keyword leaves
|
|
empty space in the list for this N additional 1st, 2nd, or 3rd
|
|
neighbors to be added. If you do not do this, you may get an error
|
|
when bonds (or molecules) are added.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If you reuse this command in an input script, you should set all
|
|
the options you need each time. This command cannot be used a 2nd
|
|
time incrementally, e.g. to add some extra storage locations via the
|
|
<em>extra</em> keyword. E.g. these two commands:</p>
|
|
</div>
|
|
<p>special_bonds lj 0.0 1.0 1.0
|
|
special_bonds coul 0.0 0.0 1.0</p>
|
|
<p>are not the same as</p>
|
|
<p>special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0</p>
|
|
<p>In the first case you end up with (after the 2nd command):</p>
|
|
<p>LJ: 0.0 0.0 0.0
|
|
Coul: coul 0.0 0.0 1.0</p>
|
|
<p>because the LJ settings are reset to their default values
|
|
each time the command is issued.</p>
|
|
<p>Likewise</p>
|
|
<pre class="literal-block">
|
|
special_bonds amber
|
|
special_bonds extra 2
|
|
</pre>
|
|
<p>is not the same as this single command:</p>
|
|
<pre class="literal-block">
|
|
special_bonds amber extra 2
|
|
</pre>
|
|
<p>since in the former case, the 2nd command will reset all the LJ and
|
|
Coulombic weights to 0.0 (the default).</p>
|
|
<p>One exception to this rule is the <em>extra</em> option itself. It is not
|
|
reset to its default value of 0 each time the special_bonds command is
|
|
invoked. This is because it can also be set by the
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> and <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> commands,
|
|
so this command will not override those settings unless you explicitly
|
|
use <em>extra</em> as an option.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a>, <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix bond/create</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0,
|
|
angle = no, dihedral = no, and extra = 0.</p>
|
|
<hr class="docutils" />
|
|
<p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
|
|
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
|
|
<p id="kremer"><strong>(Kremer)</strong> Kremer, Grest, J Chem Phys, 92, 5057 (1990).</p>
|
|
<p id="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
|
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
|
|
<p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
|
(1990).</p>
|
|
</div>
|
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