polymerist.mdtools.openfftools.physprops

For converting macroscopic parameters (such as concentration, bulk density, etc) into microscopic parameters for simulations

Functions

molecular_weight(→ openmm.unit.Quantity)	Compute the molecular weight of an RDKit Mol
offmol_mass(→ Union[openmm.unit.Quantity, ...)	Compute the molecular mass of an OpenFF Molecule (in Daltons)
offtop_mass(→ Union[openmm.unit.Quantity, ...)	Compute the molecular mass of an OpenFF Topology (in Daltons)
effective_radius(→ openmm.unit.Quantity)	Determine an effective spherical radius for a Molecule
number_density(→ openmm.unit.Quantity)	Determine the number of solvent molecules per unit volume from known physical constants
num_mols_in_box(→ int)	Return the number of particles/molecules needed to fill a box of given volume to the specified density

Module Contents

polymerist.mdtools.openfftools.physprops.molecular_weight(rdmol: rdkit.Chem.Mol, exact_isotopes: bool = False) → openmm.unit.Quantity

Compute the molecular weight of an RDKit Mol

polymerist.mdtools.openfftools.physprops.offmol_mass(offmol: openff.toolkit.Molecule, as_openmm: bool = False) → openmm.unit.Quantity | openff.units.Quantity

Compute the molecular mass of an OpenFF Molecule (in Daltons) Returns mass with OpenFF-style units, or with OpenMM-style units if as_openmm=True

polymerist.mdtools.openfftools.physprops.offtop_mass(offtop: openff.toolkit.Topology, as_openmm: bool = False) → openmm.unit.Quantity | openff.units.Quantity

Compute the molecular mass of an OpenFF Topology (in Daltons) Returns mass with OpenFF-style units, or with OpenMM-style units if as_openmm=True

polymerist.mdtools.openfftools.physprops.effective_radius(offmol: openff.toolkit.Molecule, conf_id: int = 0) → openmm.unit.Quantity

Determine an effective spherical radius for a Molecule

Defined to be the radius of the smallest sphere which contains all atoms in the molecule if that sphere is placed concentric to the centroid of the chosen conformer

polymerist.mdtools.openfftools.physprops.number_density(density: openmm.unit.Quantity, MW: openmm.unit.Quantity) → openmm.unit.Quantity

Determine the number of solvent molecules per unit volume from known physical constants For best results, provide arguments as Quantities with associated units

polymerist.mdtools.openfftools.physprops.num_mols_in_box(mol: rdkit.Chem.Mol | openff.toolkit.Molecule | openff.toolkit.Topology, box_vol: openmm.unit.Quantity, density: openmm.unit.Quantity) → int

Return the number of particles/molecules needed to fill a box of given volume to the specified density