MolecularMechanics

molsysmt.MolecularMechanics is the native data container in MolSysMT responsible for managing force field parameters, partial atomic charges, atomic masses, and non-bonded interaction settings.

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Overview and Role

As a user, molsysmt.MolecularMechanics is the object holding physical mechanics parameters required for energy evaluations, molecular dynamics simulations, or electrostatics calculations.

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Internal Attributes

Inside molsysmt.MolecularMechanics, parameters are stored as attribute arrays:

Attribute	Data Type	Description
forcefield	String	Name of the assigned forcefield (e.g. 'AMBER14', 'CHARMM36').
charge	NumPy float64 array	Partial atomic charges for each atom (n_atoms,) in elementary charge e.
mass	NumPy float64 array	Atomic masses for each atom (n_atoms,) in Da.
non_bonded_method	String	Non-bonded interaction method (e.g. 'PME', 'NoCutoff').

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Invariants and Performance

• Float64 Precision: Charges and masses use double-precision float64 for numerical accuracy during energy evaluation.

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API Documentation

Detailed methods and converters for molsysmt.MolecularMechanics are documented in the [molsysmt.MolecularMechanics API Reference].