106 lines
4.0 KiB
Plaintext
106 lines
4.0 KiB
Plaintext
"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
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Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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CHARMM, AMBER, and DREIDING force fields :h3
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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, and DREIDING force fields. Setting
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coefficients is done in the input data file via the
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"read_data"_read_data.html command or in the input script with
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commands like "pair_coeff"_pair_coeff.html or
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"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
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additional tools that can use CHARMM or AMBER to assign force field
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coefficients and convert their output into LAMMPS input.
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See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
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field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
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field.
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:link(charmm,http://www.scripps.edu/brooks)
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:link(amber,http://amber.scripps.edu)
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These style choices compute force field formulas that are consistent
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with common options in CHARMM or AMBER. See each command's
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documentation for the formula it computes.
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"bond_style"_bond_harmonic.html harmonic
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"angle_style"_angle_charmm.html charmm
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"dihedral_style"_dihedral_charmm.html charmmfsh
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"dihedral_style"_dihedral_charmm.html charmm
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"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
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"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
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"pair_style"_pair_charmm.html lj/charmm/coul/charmm
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"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
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"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
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"special_bonds"_special_bonds.html charmm
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"special_bonds"_special_bonds.html amber :ul
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NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
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released in March 2017. We recommend they be used instead of the
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older {charmm} styles. See discussion of the differences on the "pair
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charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
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doc pages.
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DREIDING is a generic force field developed by the "Goddard
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group"_http://www.wag.caltech.edu at Caltech and is useful for
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predicting structures and dynamics of organic, biological and
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main-group inorganic molecules. The philosophy in DREIDING is to use
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general force constants and geometry parameters based on simple
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hybridization considerations, rather than individual force constants
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and geometric parameters that depend on the particular combinations of
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atoms involved in the bond, angle, or torsion terms. DREIDING has an
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"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
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interactions involving a hydrogen atom on very electronegative atoms
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(N, O, F).
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See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
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These style choices compute force field formulas that are consistent
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with the DREIDING force field. See each command's
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documentation for the formula it computes.
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"bond_style"_bond_harmonic.html harmonic
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"bond_style"_bond_morse.html morse :ul
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"angle_style"_angle_harmonic.html harmonic
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"angle_style"_angle_cosine.html cosine
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"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
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"dihedral_style"_dihedral_charmm.html charmm
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"improper_style"_improper_umbrella.html umbrella :ul
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"pair_style"_pair_buck.html buck
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"pair_style"_pair_buck.html buck/coul/cut
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"pair_style"_pair_buck.html buck/coul/long
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"pair_style"_pair_lj.html lj/cut
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"pair_style"_pair_lj.html lj/cut/coul/cut
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"pair_style"_pair_lj.html lj/cut/coul/long :ul
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"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
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"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
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"special_bonds"_special_bonds.html dreiding :ul
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:line
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:link(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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:link(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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:link(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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