forked from lijiext/lammps
142 lines
4.4 KiB
Plaintext
142 lines
4.4 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 1 120.0 1 60 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) <MacKerell>` for a description of the CHARMM force
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field. This dihedral style can also be used for the AMBER force field
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(see comment on weighting factors below). See :ref:`(Cornell) <Cornell>`
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for a description of the AMBER force 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 (0.0 to 1.0)
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The weighting factor is applied to pairwise interaction between the
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1st and 4th atoms in the dihedral, which are computed by a CHARMM
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:doc:`pair_style <pair_charmm>` with epsilon and sigma values specified
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with a :doc:`pair_coeff <pair_charmm>` command. Note that this
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weighting factor is unrelated to the weighting factor specified by the
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:doc:`special bonds <special_bonds>` command which applies to all 1-4
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interactions in the system.
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For CHARMM force fields, the special_bonds 1-4 weighting factor should
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be set to 0.0. This is because the pair styles that contain "charmm"
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(e.g. :doc:`pair_style lj/charmm/coul/long <pair_charmm>`) define extra
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1-4 interaction coefficients that are used by this dihedral style to
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compute those interactions explicitly. This means that if any of the
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weighting factors defined as dihedral coefficients (4th coeff above)
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are non-zero, then you must use a charmm pair style. Note that if you
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do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
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default) then 1-4 interactions in dihedrals will be computed twice,
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once by the pair routine and once by the dihedral routine, which is
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probably not what you want.
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For AMBER force fields, the special_bonds 1-4 weighting factor should
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be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
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weighting factors (4th coeff above) should be set to 0.0. In this
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case, you can use any pair style you wish, since the dihedral does not
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need any 1-4 information.
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----------
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Styles with a *cuda*, *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 USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if 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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.. _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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.. _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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