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reword and reformat text in Howto_bioFF.txt a little bit. add warnings about msi2lmp's age and lack of maintenance
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Axel Kohlmeyer
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@ -7,29 +7,31 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
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:line
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CHARMM, AMBER, COMPASS and DREIDING force fields :h3
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CHARMM, AMBER, COMPASS, 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, COMPASS 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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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 "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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"bond_coeff"_bond_coeff.html and so on. See the "Tools"_Tools.html 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 "(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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field. See "(Cornell)"_#howto-Cornell for a description of the AMBER
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force field. See "(Sun)"_#howto-Sun for a description of the COMPASS
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force 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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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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"bond_style"_bond_harmonic.html harmonic
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"angle_style"_angle_charmm.html charmm
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@ -44,21 +46,26 @@ documentation for the formula it computes.
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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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NOTE: 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 "pair
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charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html doc
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pages.
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COMPASS is a general force field for atomistic simulation of
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common organic molecules, inorganic small molecules, and polymers which
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was developed using ab initio and empirical parametrization techniques.
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See the "Tools"_Tools.html doc page for the msi2lmp tool for creating
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LAMMPS template input and data files from BIOVIA’s Materias Studio files.
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See "(Sun)"_#howto-Sun for a description of the COMPASS force field.
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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 "Tools"_Tools.html doc 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 "(Sun)"_#howto-Sun for a description of the COMPASS force
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field.
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These style choices compute force field formulas that are consistent
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with the COMPASS force field. See each command's
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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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"bond_style"_bond_class2.html class2
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@ -74,20 +81,19 @@ documentation for the formula it computes.
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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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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 "explicit hydrogen
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bond term"_pair_hbond_dreiding.html to describe interactions involving a
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hydrogen atom on very electronegative atoms (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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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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"bond_style"_bond_harmonic.html harmonic
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