134 lines
5.6 KiB
ReStructuredText
134 lines
5.6 KiB
ReStructuredText
CHARMM, AMBER, COMPASS, and DREIDING force fields
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=================================================
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A force field has 2 parts: the formulas that define it and the
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coefficients used for a particular system. Here we only discuss
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formulas implemented in LAMMPS that correspond to formulas commonly
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used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
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coefficients is done either from special sections in an input data file
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via the :doc:`read_data <read_data>` command or in the input script with
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commands like :doc:`pair_coeff <pair_coeff>` or
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:doc:`bond_coeff <bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc
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page for additional tools that can use CHARMM, AMBER, or Materials
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Studio generated files to assign force field coefficients and convert
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their output into LAMMPS input.
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See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
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field. See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER
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force field. See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS
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force field.
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.. _charmm: http://www.scripps.edu/brooks
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.. _amber: http://amber.scripps.edu
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The interaction styles listed below compute force field formulas that
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are consistent with common options in CHARMM or AMBER. See each
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command's documentation for the formula it computes.
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* :doc:`bond_style <bond_harmonic>` harmonic
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* :doc:`angle_style <angle_charmm>` charmm
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* :doc:`dihedral_style <dihedral_charmm>` charmmfsh
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* :doc:`dihedral_style <dihedral_charmm>` charmm
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* :doc:`pair_style <pair_charmm>` lj/charmmfsw/coul/charmmfsh
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* :doc:`pair_style <pair_charmm>` lj/charmmfsw/coul/long
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* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm
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* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm/implicit
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* :doc:`pair_style <pair_charmm>` lj/charmm/coul/long
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* :doc:`special_bonds <special_bonds>` charmm
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* :doc:`special_bonds <special_bonds>` amber
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.. note::
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For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released
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in March 2017. We recommend they be used instead of the older *charmm*
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styles. See discussion of the differences on the :doc:`pair charmm <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
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pages.
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COMPASS is a general force field for atomistic simulation of common
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organic molecules, inorganic small molecules, and polymers which was
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developed using ab initio and empirical parameterization techniques.
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See the :doc:`Tools <Tools>` page for the msi2lmp tool for creating
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LAMMPS template input and data files from BIOVIA's Materials Studio
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files. Please note that the msi2lmp tool is very old and largely
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unmaintained, so it does not support all features of Materials Studio
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provided force field files, especially additions during the last decade.
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You should watch the output carefully and compare results, where
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possible. See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS force
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field.
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These interaction styles listed below compute force field formulas that
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are consistent with the COMPASS force field. See each command's
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documentation for the formula it computes.
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* :doc:`bond_style <bond_class2>` class2
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* :doc:`angle_style <angle_class2>` class2
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* :doc:`dihedral_style <dihedral_class2>` class2
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* :doc:`improper_style <improper_class2>` class2
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* :doc:`pair_style <pair_class2>` lj/class2
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* :doc:`pair_style <pair_class2>` lj/class2/coul/cut
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* :doc:`pair_style <pair_class2>` lj/class2/coul/long
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* :doc:`special_bonds <special_bonds>` lj/coul 0 0 1
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DREIDING is a generic force field developed by the `Goddard group <http://www.wag.caltech.edu>`_ at Caltech and is useful for
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predicting structures and dynamics of organic, biological and main-group
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inorganic molecules. The philosophy in DREIDING is to use general force
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constants and geometry parameters based on simple hybridization
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considerations, rather than individual force constants and geometric
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parameters that depend on the particular combinations of atoms involved
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in the bond, angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond term <pair_hbond_dreiding>` to describe interactions involving a
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hydrogen atom on very electronegative atoms (N, O, F).
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See :ref:`(Mayo) <howto-Mayo>` for a description of the DREIDING force field
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The interaction styles listed below compute force field formulas that
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are consistent with the DREIDING force field. See each command's
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documentation for the formula it computes.
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* :doc:`bond_style <bond_harmonic>` harmonic
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* :doc:`bond_style <bond_morse>` morse
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* :doc:`angle_style <angle_cosine_squared>` cosine/squared
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* :doc:`angle_style <angle_harmonic>` harmonic
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* :doc:`angle_style <angle_cosine>` cosine
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* :doc:`angle_style <angle_cosine_periodic>` cosine/periodic
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* :doc:`dihedral_style <dihedral_charmm>` charmm
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* :doc:`improper_style <improper_umbrella>` umbrella
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* :doc:`pair_style <pair_buck>` buck
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* :doc:`pair_style <pair_buck>` buck/coul/cut
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* :doc:`pair_style <pair_buck>` buck/coul/long
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* :doc:`pair_style <pair_lj>` lj/cut
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* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut
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* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long
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* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/lj
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* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/morse
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* :doc:`special_bonds <special_bonds>` dreiding
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----------
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.. _howto-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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.. _howto-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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.. _howto-Sun:
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**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
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.. _howto-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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