165 lines
6.0 KiB
ReStructuredText
165 lines
6.0 KiB
ReStructuredText
.. index:: dihedral_style charmm
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.. index:: dihedral_style charmm/intel
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.. index:: dihedral_style charmm/kk
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.. index:: dihedral_style charmm/omp
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.. index:: dihedral_style charmmfsw
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dihedral_style charmm command
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=============================
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Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
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dihedral_style charmmfsw 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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dihedral_style style
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* style = *charmm* or *charmmfsw*
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Examples
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""""""""
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.. code-block:: LAMMPS
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dihedral_style charmm
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dihedral_style charmmfsw
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dihedral_coeff 1 0.2 1 180 1.0
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dihedral_coeff 2 1.8 1 0 1.0
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dihedral_coeff 1 3.1 2 180 0.5
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Description
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"""""""""""
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The *charmm* and *charmmfsw* dihedral styles use the potential
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.. math::
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E = K [ 1 + \cos (n \phi - d) ]
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See :ref:`(MacKerell) <dihedral-MacKerell>` for a description of the CHARMM
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force field. This dihedral style can also be used for the AMBER force
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field (see comment on weighting factors below). See
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:ref:`(Cornell) <dihedral-Cornell>` for a description of the AMBER force
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field.
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.. note::
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The newer *charmmfsw* style was released in March 2017. We
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recommend it be used instead of the older *charmm* style when running
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a simulation with the CHARMM force field, either with long-range
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Coulombics or a Coulombic cutoff, via the :doc:`pair_style lj/charmmfsw/coul/long <pair_charmm>` and :doc:`pair_style lj/charmmfsw/coul/charmmfsh <pair_charmm>` commands respectively.
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Otherwise the older *charmm* style is fine to use. See the discussion
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below and more details on the :doc:`pair_style charmm <pair_charmm>` doc
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page.
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The following coefficients must be defined for each dihedral type via the
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:doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
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the data file or restart files read by the :doc:`read_data <read_data>`
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or :doc:`read_restart <read_restart>` commands:
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* :math:`K` (energy)
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* :math:`n` (integer >= 0)
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* :math:`d` (integer value of degrees)
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* weighting factor (1.0, 0.5, or 0.0)
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The weighting factor is required to correct for double counting
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pairwise non-bonded Lennard-Jones interactions in cyclic systems or
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when using the CHARMM dihedral style with non-CHARMM force fields.
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With the CHARMM dihedral style, interactions between the first and fourth
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atoms in a dihedral are skipped during the normal non-bonded force
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computation and instead evaluated as part of the dihedral using
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special epsilon and sigma values specified with the
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:doc:`pair_coeff <pair_charmm>` command of pair styles that contain
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"lj/charmm" (e.g. :doc:`pair_style lj/charmm/coul/long <pair_charmm>`)
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In 6-membered rings, the same 1-4 interaction would be computed twice
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(once for the clockwise 1-4 pair in dihedral 1-2-3-4 and once in the
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counterclockwise dihedral 1-6-5-4) and thus the weighting factor has
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to be 0.5 in this case. In 4-membered or 5-membered rings, the 1-4
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dihedral also is counted as a 1-2 or 1-3 interaction when going around
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the ring in the opposite direction and thus the weighting factor is
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0.0, as the 1-2 and 1-3 exclusions take precedence.
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Note that this dihedral weighting factor is unrelated to the scaling
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factor specified by the :doc:`special bonds <special_bonds>` command
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which applies to all 1-4 interactions in the system. For CHARMM force
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fields, the special_bonds 1-4 interaction scaling factor should be set
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to 0.0. Since the corresponding 1-4 non-bonded interactions are
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computed with the dihedral. This means that if any of the weighting
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factors defined as dihedral coefficients (fourth coeff above) are
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non-zero, then you must use a pair style with "lj/charmm" and set the
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special_bonds 1-4 scaling factor to 0.0 (which is the
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default). Otherwise 1-4 non-bonded interactions in dihedrals will be
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computed twice.
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For simulations using the CHARMM force field with a Coulombic cutoff,
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the difference between the *charmm* and *charmmfsw* styles is in the
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computation of the 1-4 non-bond interactions, though only if the
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distance between the two atoms is within the switching region of the
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pairwise potential defined by the corresponding CHARMM pair style,
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i.e. within the outer cutoff specified for the pair style. The
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*charmmfsw* style should only be used when using the corresponding
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:doc:`pair_style lj/charmmfsw/coul/charmmfsw <pair_charmm>` or
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:doc:`pair_style lj/charmmfsw/coul/long <pair_charmm>` commands. Use
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the *charmm* style with the older :doc:`pair_style <pair_charmm>`
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commands that have just "charmm" in their style name. See the
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discussion on the :doc:`CHARMM pair_style <pair_charmm>` page for
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details.
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Note that for AMBER force fields, which use pair styles with "lj/cut",
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the special_bonds 1-4 scaling factor should be set to the AMBER
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defaults (1/2 and 5/6) and all the dihedral weighting factors (fourth
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coeff above) must be set to 0.0. In this case, you can use any pair
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style you wish, since the dihedral does not need any Lennard-Jones
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parameter information and will not compute any 1-4 non-bonded
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interactions. Likewise the *charmm* or *charmmfsw* styles are
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identical in this case since no 1-4 non-bonded interactions are
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computed.
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----------
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.. include:: accel_styles.rst
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----------
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Restrictions
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""""""""""""
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When using run_style :doc:`respa <run_style>`, these dihedral styles
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must be assigned to the same r-RESPA level as *pair* or *outer*\ .
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When used in combination with CHARMM pair styles, the 1-4
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:doc:`special_bonds <special_bonds>` scaling factors must be set to 0.0.
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Otherwise non-bonded contributions for these 1-4 pairs will be
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computed multiple times.
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These dihedral styles can only be used if LAMMPS was built with the
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MOLECULE package. See the :doc:`Build package <Build_package>` doc page
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for more info.
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Related commands
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""""""""""""""""
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:doc:`dihedral_coeff <dihedral_coeff>`
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Default
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"""""""
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none
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----------
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.. _dihedral-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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.. _dihedral-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 B, 102, 3586 (1998).
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