Molecular Mechanics Data

MolSysMT standardizes molecular mechanics forcefields, implicit solvent models, non-bonded interaction parameters, and constraint options across simulation engines.

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Forcefields and Water Models

Recognized forcefield architectures, explicit water models, and atom-level parameter attributes:

Attribute / Property	Scope / Options	Description	Canonical Unit
forcefield	AMBER14, CHARMM36, OpenFF, GROMOS, OPLS-AA	Force field parameter definition string or object.	N/A
water_model	TIP3P, TIP4P, TIP4P-Ew, TIP5P, SPC, SPC/E, OPC	Explicit solvent model specification.	N/A
atom_ff_type	Atom	Forcefield-assigned atom type name.	N/A
partial_charge	Atom	Fractional atomic point charge.	elementary_charge (e)

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Non-Bonded and Continuum Solvent Settings

Cutoff parameters, electrostatics algorithms, and continuum dielectric properties:

Attribute / Property	Scope / Options	Description	Canonical Unit
non_bonded_method	NoCutoff, CutoffNonPeriodic, CutoffPeriodic, PME, LJPME	Non-bonded interaction algorithm.	N/A
cutoff_distance	Real positive quantity	Direct-space non-bonded interaction cutoff.	nanometer (nm)
switch_distance	Real positive quantity	Distance at which non-bonded switching function begins.	nanometer (nm)
implicit_solvent	OBC1, OBC2, GBn, GBn2, HCT, GB	Implicit continuum solvent model.	N/A
salt_concentration	Real positive quantity	Ionic strength for Debye-Hückel / Generalized Born screening.	molar (M)
solute_dielectric	Real positive scalar	Relative dielectric permittivity inside the solute cavity (solute dielectric).	N/A
solvent_dielectric	Real positive scalar	Relative dielectric permittivity of bulk solvent (solvent dielectric).	N/A
dispersion_correction	Boolean	Analytical long-range dispersion correction for energy and pressure.	N/A
ewald_error_tolerance	Real positive scalar	Target relative error tolerance for PME / Ewald direct-space sum.	N/A

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Constraints and Integration Parameters

Geometric constraints, rigid water settings, and mass repartitioning:

Attribute / Property	Scope / Options	Description	Canonical Unit
constraints	None, HBonds, AllBonds, HAngles	Geometric distance constraint policy.	N/A
flexible_constraints	Boolean	Policy allowing constrained bonds to vibrate harmonically.	N/A
rigid_water	Boolean	Enforces rigid geometry on tri-atomic water molecules.	N/A
hydrogen_mass	Real positive quantity	Mass repartitioning value assigned to hydrogen atoms for integration stability.	dalton (Da)