forked from lijiext/lammps
156 lines
5.2 KiB
Plaintext
156 lines
5.2 KiB
Plaintext
.. index:: dihedral_style charmm
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dihedral_style charmm command
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=============================
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dihedral_style charmm/intel command
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===================================
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dihedral_style charmm/kk command
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================================
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dihedral_style charmm/omp command
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=================================
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Syntax
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""""""
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.. parsed-literal::
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dihedral_style charmm
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Examples
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""""""""
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.. parsed-literal::
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dihedral_style charmm
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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* dihedral style uses the potential
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.. image:: Eqs/dihedral_charmm.jpg
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:align: center
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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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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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* K (energy)
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* n (integer >= 0)
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* 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 1st and 4th
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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 (4th 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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Also note that for AMBER force fields, which use pair styles with
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"lj/cut", the special_bonds 1-4 scaling factor should be set to the
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AMBER defaults (1/2 and 5/6) and all the dihedral weighting factors
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(4th coeff above) must be set to 0.0. In this case, you can use any
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pair style you wish, since the dihedral does not need any
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Lennard-Jones parameter information and will not compute any 1-4
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non-bonded interactions.
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----------
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Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
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use the :doc:`suffix <suffix>` command in your input script.
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See :doc:`Section_accelerate <Section_accelerate>` of the manual for
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more instructions on how to use the accelerated styles effectively.
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----------
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Restrictions
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""""""""""""
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This dihedral style can only be used if LAMMPS was built with the
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MOLECULE package (which it is by default). See the :ref:`Making LAMMPS <start_3>` section for more info on packages.
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Related commands
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""""""""""""""""
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:doc:`dihedral_coeff <dihedral_coeff>`
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**Default:** 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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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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