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Merge pull request #1409 from akohlmey/collected-small-changes

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Collected small changes and bugfixes for the next patch release
This commit is contained in:
Axel Kohlmeyer
2019-04-05 15:39:16 -04:00
committed by GitHub
parent ed90596849 05993a79b8
commit ac7312caf1
29 changed files with 177 additions and 115 deletions
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2
doc/src/Howto.txt
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@ -148,7 +148,7 @@ END_RST -->
<!-- HTML_ONLY -->
"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
"CHARMM, AMBER, COMPASS, and DREIDING force fields"_Howto_bioFF.html
"TIP3P water model"_Howto_tip3p.html
"TIP4P water model"_Howto_tip4p.html
"SPC water model"_Howto_spc.html :all(b)

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doc/src/Howto_bioFF.txt
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@ -7,29 +7,31 @@ 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
coefficients is done in the input data file via the
"read_data"_read_data.html command or in the input script with
used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
coefficients is done either from special sections in an 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
"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
"bond_coeff"_bond_coeff.html and so on. See the "Tools"_Tools.html doc
page for additional tools that can use CHARMM, AMBER, or Materials
Studio generated files to assign force field coefficients and convert
their output into LAMMPS input.
See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
field.
field. See "(Cornell)"_#howto-Cornell for a description of the AMBER
force field. See "(Sun)"_#howto-Sun for a description of the COMPASS
force field.
:link(charmm,http://www.scripps.edu/brooks)
:link(amber,http://amber.scripps.edu)
These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command's
documentation for the formula it computes.
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
command's documentation for the formula it computes.
"bond_style"_bond_harmonic.html harmonic
"angle_style"_angle_charmm.html charmm
@ -44,28 +46,54 @@ documentation for the formula it computes.
"special_bonds"_special_bonds.html charmm
"special_bonds"_special_bonds.html amber :ul
NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
released in March 2017. We recommend they be used instead of the
older {charmm} styles. See discussion of the differences on the "pair
charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
doc pages.
NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were released
in March 2017. We recommend they be used instead of the 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 parameterization techniques.
See the "Tools"_Tools.html doc page for the msi2lmp tool for creating
LAMMPS template input and data files from BIOVIA’s Materials Studio
files. Please note that the msi2lmp tool is very old and largely
unmaintained, so it does not support all features of Materials Studio
provided force field files, especially additions during the last decade.
You should watch the output carefully and compare results, where
possible. See "(Sun)"_#howto-Sun for a description of the COMPASS force
field.
These interaction styles listed below 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
main-group inorganic molecules. The philosophy in DREIDING is to use
general force constants and geometry parameters based on simple
hybridization considerations, rather than individual force constants
and geometric parameters that depend on the particular combinations of
atoms involved in the bond, angle, or torsion terms. DREIDING has an
"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).
predicting structures and dynamics of organic, biological and main-group
inorganic molecules. The philosophy in DREIDING is to use general force
constants and geometry parameters based on simple hybridization
considerations, rather than individual force constants and geometric
parameters that depend on the particular combinations of atoms involved
in the bond, angle, or torsion terms. DREIDING has an "explicit hydrogen
bond term"_pair_hbond_dreiding.html to describe interactions involving a
hydrogen atom on very electronegative atoms (N, O, F).
See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command's
The interaction styles listed below compute force field formulas that
are consistent with the DREIDING force field. See each command's
documentation for the formula it computes.
"bond_style"_bond_harmonic.html harmonic
@ -100,6 +128,9 @@ 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).

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doc/src/Howto_tip3p.txt
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@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
TIP3P water model :h3
The TIP3P water model as implemented in CHARMM
"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
"(MacKerell)"_#howto-tip3p specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -60,6 +60,10 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
:link(howto-tip3p)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
:link(Jorgensen1)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).