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Include info for COMPASS in the Howto section

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Evangelos Voyiatzis 2019-04-05 15:50:58 +02:00 committed by GitHub
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doc/src/Howto_bioFF.txt
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@ -7,12 +7,12 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
CHARMM, AMBER, and DREIDING force fields :h3
CHARMM, AMBER, COMPASS and DREIDING force fields :h3
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, and DREIDING force fields. Setting
used in the CHARMM, AMBER, COMPASS and DREIDING force fields. Setting
coefficients is done in the input data file via the
"read_data"_read_data.html command or in the input script with
commands like "pair_coeff"_pair_coeff.html or
@ -50,6 +50,28 @@ older {charmm} styles. See discussion of the differences on the "pair
charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
doc pages.
COMPASS is a general force field for atomistic simulation of
common organic molecules, inorganic small molecules, and polymers which
was developed using ab initio and empirical parametrization techniques.
See the "Tools"_Tools.html doc page for the msi2lmp tool for creating
LAMMPS template input and data files from BIOVIA’s Materias Studio files.
See "(Sun)"_#howto-Sun for a description of the COMPASS force field.
These style choices compute force field formulas that are consistent
with the COMPASS force field. See each command's
documentation for the formula it computes.
"bond_style"_bond_class2.html class2
"angle_style"_angle_class2.html class2
"dihedral_style"_dihedral_class2.html class2
"improper_style"_improper_class2.html class2 :ul
"pair_style"_pair_class2.html lj/class2
"pair_style"_pair_class2.html lj/class2/coul/cut
"pair_style"_pair_class2.html lj/class2/coul/long :ul
"special_bonds"_special_bonds.html lj/coul 0 0 1 :ul
DREIDING is a generic force field developed by the "Goddard
group"_http://www.wag.caltech.edu at Caltech and is useful for
predicting structures and dynamics of organic, biological and
@ -100,6 +122,9 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(howto-Sun)
[(Sun)] Sun, J. Phys. Chem. B, 102, 7338–7364 (1998).
:link(howto-Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).