diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt index ee53420723..b6995920ae 100644 --- a/doc/src/Howto_bioFF.txt +++ b/doc/src/Howto_bioFF.txt @@ -7,29 +7,31 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -CHARMM, AMBER, COMPASS 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, 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 +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 @@ -44,21 +46,26 @@ 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 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. +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 style choices compute force field formulas that are consistent -with the COMPASS force field. See each command's +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 @@ -74,20 +81,19 @@ documentation for the formula it computes. 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