275 lines
11 KiB
ReStructuredText
275 lines
11 KiB
ReStructuredText
.. index:: special_bonds
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special_bonds command
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=====================
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Syntax
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""""""
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.. code-block:: LAMMPS
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special_bonds keyword values ...
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* one or more keyword/value pairs may be appended
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* keyword = *amber* or *charmm* or *dreiding* or *fene* or *lj/coul* or *lj* or *coul* or *angle* or *dihedral*
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.. parsed-literal::
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*amber* values = none
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*charmm* values = none
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*dreiding* values = none
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*fene* values = none
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*lj/coul* 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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*lj* 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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*coul* 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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*angle* value = *yes* or *no*
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*dihedral* value = *yes* or *no*
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Examples
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""""""""
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.. code-block:: LAMMPS
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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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Description
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"""""""""""
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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 :doc:`pair styles <pair_style>` 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 :doc:`read_data <read_data>` command. Typically a
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:doc:`bond_style <bond_style>` 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).
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.. note::
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These weighting factors are NOT used by :doc:`pair styles <pair_style>` 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 :doc:`pair_style hybrid <pair_hybrid>` command.
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Thus LAMMPS ignores special_bonds settings when many-body potentials
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are calculated. Please note, that the existence of explicit bonds
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for atoms that are described by a many-body potential will alter the
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neighbor list and thus can render the computation of those interactions
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invalid, since those pairs are not only used to determine direct
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pairwise interactions but also neighbors of neighbors and more.
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The recommended course of action is to remove such bonds, or - if
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that is not possible - use a special bonds setting of 1.0 1.0 1.0.
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.. note::
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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.
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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.
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The first 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 second 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 third coefficient is the weighting factor on 1-4
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atom pairs which are those separated by 3 bonds (e.g. the first and fourth
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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.
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.. note::
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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 :doc:`read_data <read_data>` or
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:doc:`read_restart <read_restart>` 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.
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The two exceptions to this rule are (a) if the *angle* or *dihedral*
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keywords are set to *yes* (see below), or (b) if the
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:doc:`delete_bonds <delete_bonds>` command is used with the *special*
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option that re-computes the 1-2,1-3,1-4 topologies after bonds are
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deleted; see the :doc:`delete_bonds <delete_bonds>` command for more
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details.
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The *amber* 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 :ref:`(Cornell) <Cornell>` for a
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description of the AMBER force field.
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The *charmm* 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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*lj/charmm/coul/charmm* and *lj/charmm/coul/long* 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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:doc:`pair_coeff <pair_coeff>` and :doc:`dihedral_style <dihedral_style>`
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commands for more information. See :ref:`(MacKerell) <MacKerell>` for a
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description of the CHARMM force field.
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The *dreiding* 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 :ref:`(Mayo) <Mayo>`.
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The *fene* 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 :doc:`FENE bonds <bond_fene>`. See
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:ref:`(Kremer) <Kremer>` for a description of FENE bonds.
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The *lj/coul*, *lj*, and *coul* keywords allow the 3 coefficients to
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be set explicitly. The *lj/coul* keyword sets both the LJ and
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Coulombic coefficients to the same 3 values. The *lj* and *coul*
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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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The *angle* 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 *angle* keyword is specified as *yes*, 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 *angle* keyword is specified as *no* which is the
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default, then the 2,4 interaction will also be weighted by 0.5.
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The *dihedral* 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 *dihedral* keyword is specified as *yes*, 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 *dihedral* keyword is specified as *no* which is the
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default, then the 2,5 interaction will also be weighted by 0.5.
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----------
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.. note::
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LAMMPS stores and maintains a data structure with a list of the
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first, second, and third 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 first neighbor
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but may also induce \*many\* new second and third neighbors, depending on the
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molecular topology of your system. Using the *extra/special/per/atom*
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keyword to either :doc:`read_data <read_data>` or :doc:`create_box <create_box>`
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reserves empty space in the list for this N additional first, second, or third
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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.
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----------
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.. note::
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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 second
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time incrementally. E.g. these two commands:
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.. code-block:: LAMMPS
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special_bonds lj 0.0 1.0 1.0
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special_bonds coul 0.0 0.0 1.0
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are not the same as
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.. code-block:: LAMMPS
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special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0
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In the first case you end up with (after the second command):
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.. parsed-literal::
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LJ: 0.0 0.0 0.0
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Coul: 0.0 0.0 1.0
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while only in the second case, you get the desired settings of:
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.. parsed-literal::
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LJ: 0.0 1.0 1.0
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Coul: 0.0 0.0 1.0
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This happens because the LJ (and Coul) settings are reset to
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their default values before modifying them, each time the
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*special_bonds* command is issued.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`delete_bonds <delete_bonds>`, :doc:`fix bond/create <fix_bond_create>`
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Default
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"""""""
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All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0,
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angle = no, dihedral = no.
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----------
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.. _Cornell:
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**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
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Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
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.. _Kremer:
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**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
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.. _MacKerell:
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**(MacKerell)** 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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.. _Mayo:
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**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
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(1990).
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