Glossary#

One-line definitions for terms used throughout these docs.

Bespoke parameter: A force field parameter generated specifically for the user's molecule(s) of interest, with a SMIRKS pattern derived from the actual atomic connectivity.
Congeneric series: A set of related molecules sharing a common scaffold. In presto, congeneric fits share parameters across the series wherever SMIRKS overlap (controlled by max_extend_distance).
Interchange: OpenFF's intermediate representation between SMIRNOFF and downstream MD engines. Produced by ForceField.create_interchange(topology).
Linearised harmonics: Harmonic bond/angle parameters reparametrised as two linear coefficients to stabilise fitting. See the footnote in Method overview.
MLP (machine learning potential): A neural-network model trained on QM energies and forces, used as a fast surrogate for QM during sampling and force-field fitting.
MSM (modified Seminario method): An algorithm for deriving bond and angle force constants and equilibrium values from the molecular Hessian. See the paper.
offxml: The XML serialisation of a SMIRNOFF force field. Produced by OpenFF and consumed by anything that parses SMIRNOFF.
SMIRNOFF: OpenFF's force field format. Parameters are organised into handlers (Bonds, Angles, …) and matched to atoms via SMIRKS.
SMIRKS: Often used to mean a SMARTS pattern with numerical atom-index tags. presto generates one bespoke SMIRKS per bond/angle/torsion in your molecule.
Type generation: The process of building bespoke SMIRKS patterns for a molecule's valence terms. Controlled by param_settings.type_generation_settings.
Valence parameter: A force-field parameter governing bonded interactions: bonds, angles, proper torsions, or improper torsions. presto only fits valence parameters.
Well-tempered metadynamics: A metadynamics variant where the bias height decays over time according to a bias_factor. Used in mm_md_metadynamics* protocols to enhance torsion sampling. See the paper.