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8.4.1. 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 (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.

(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).