diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index ec90472c27..cdc4efd737 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -66,6 +66,7 @@ Force fields howto :name: force_howto :maxdepth: 1 + Howto_FFgeneral Howto_bioFF Howto_amoeba Howto_tip3p diff --git a/doc/src/Howto_FFgeneral.rst b/doc/src/Howto_FFgeneral.rst new file mode 100644 index 0000000000..1b96ae1119 --- /dev/null +++ b/doc/src/Howto_FFgeneral.rst @@ -0,0 +1,55 @@ +Some general force field considerations +======================================= + +A compact summary of the concepts, definitions, and properties of force +fields with explicit bonded interactions (like the ones discussed in +this HowTo) is given in :ref:`(Gissinger) `. + +A force field has 2 parts: the formulas that define its potential +functions and the coefficients used for a particular system. To assign +parameters it is first required to assign atom types. Those are not +only based on the elements, but also on the chemical environment due to +the atoms bound to them. This often follows the chemical concept of +*functional groups*. Example: a carbon atom bound with a single bond to +a single OH-group (alcohol) would be a different atom type than a carbon +atom bound to a methyl CH3 group (aliphatic carbon). The atom types +usually then determine the non-bonded Lennard-Jones parameters and the +parameters for bonds, angles, dihedrals, and impropers. On top of that, +partial charges have to be applied. Those are usually independent of +the atom types and are determined either for groups of atoms called +residues with some fitting procedure based on quantum mechanical +calculations, or based on some increment system that add or subtract +increments from the partial charge of an atom based on the types of +the neighboring atoms. + +Force fields differ in the strategies they employ to determine the +parameters and charge distribution in how generic or specific they are +which in turn has an impact on the accuracy (compare for example +CGenFF to CHARMM and GAFF to Amber). Because of the different +strategies, it is not a good idea to use a mix of parameters from +different force field *families* (like CHARMM, Amber, or GROMOS) +and that extends to the parameters for the solvent, especially +water. The publication describing the parameterization of a force +field will describe which water model to use. Changing the water +model usually leads to overall worse results (even if it may improve +on the water itself). + +In addition, one has to consider that *families* of force fields like +CHARMM, Amber, OPLS, or GROMOS have evolved over time and thus provide +different *revisions* of the force field parameters. These often +corresponds to changes in the functional form or the parameterization +strategies. This may also result in changes required for simulation +settings like the preferred cutoff or how Coulomb interactions are +computed (cutoff, smoothed/shifted cutoff, or long-range with Ewald +summation or equivalent). Unless explicitly stated in the publication +describing the force field, the Coulomb interaction cannot be chosen at +will but must match the revision of the force field. That said, +liberties may be taken during the initial equilibration of a system to +speed up the process, but not for production simulations. + +---------- + +.. _Typelabel2: + +**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024). + diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index 92dd45b9b6..cf8e4ab13e 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -1,22 +1,16 @@ CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields ======================================================= -A compact summary of the concepts, definitions, and properties of -force fields with explicit bonded interactions (like the ones discussed -in this HowTo) is given in :ref:`(Gissinger) `. - -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 either from special sections in an input data file -via the :doc:`read_data ` command or in the input script with -commands like :doc:`pair_coeff ` or :doc:`bond_coeff -` and so on. See the :doc:`Tools ` 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. LAMMPS input scripts can also be generated by -`charmm-gui.org `_. +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 either from special sections in an +input data file via the :doc:`read_data ` command or in the +input script with commands like :doc:`pair_coeff ` or +:doc:`bond_coeff ` and so on. See the :doc:`Tools ` +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. LAMMPS input scripts can also be +generated by `charmm-gui.org `_. CHARMM and AMBER ---------------- @@ -203,9 +197,11 @@ 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 :doc:`explicit hydrogen bond term ` to describe interactions involving a -hydrogen atom on very electronegative atoms (N, O, F). Unlike CHARMM -or AMBER, the DREIDING force field has not been parameterized for -considering solvents (like water). +hydrogen atom on very electronegative atoms (N, O, F). Unlike CHARMM or +AMBER, the DREIDING force field has not been parameterized for +considering solvents (like water) and has no rules for assigning +(partial) charges. That will seriously limit its accuracy when used for +simulating systems where those matter. See :ref:`(Mayo) ` for a description of the DREIDING force field @@ -272,10 +268,6 @@ compatible with a subset of OPLS interactions. ---------- -.. _Typelabel2: - -**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024). - .. _howto-MacKerell: **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998). J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst index 00bd8a1b10..f84d7797d2 100644 --- a/doc/src/Howto_spc.rst +++ b/doc/src/Howto_spc.rst @@ -1,5 +1,5 @@ -SPC water model -=============== +SPC and SPC/E water model +========================= The SPC water model specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the three atoms. diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 5f38ea3c62..76c470d615 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -212,11 +212,11 @@ file changed): When constructing an OPC model, we cannot use the ``tip3p.mol`` file due to the different geometry. Below is a molecule file providing the 3 -sites for an implicit OPC geometry with TIP4P styles. Note, that the -"Shake" and "Special" sections are missing here. Those will be -auto-generated since the molecule file is loaded *after* the simulation -box has been created. They are required only when the molecule file -is loaded *before*. +sites of an implicit OPC geometry for use with TIP4P styles. Note, that +the "Shake" and "Special" sections are missing here. Those will be +auto-generated by LAMMPS when the molecule file is loaded *after* the +simulation box has been created. These sections are required only when +the molecule file is loaded *before*. .. _opc3p_molecule: .. code-block::