Source code for gmso.external.convert_openmm

"""Convert to and from an OpenMM Topology or System object."""

import unyt as u

from import has_openmm, has_openmm_unit, import_

if has_openmm & has_openmm_unit:
    openmm_unit = import_("openmm.unit")
    from openmm import *
    from import *

[docs] def to_openmm(topology, openmm_object="topology"): """Convert an untyped topology object to an untyped OpenMM modeller or topology. This is useful if it's preferred to atom-type a system within OpenMM. See for more information. Parameters ---------- topology : `Topology` object An untyped topology object open_mm_object : 'topology' or 'modeller' OpenMM object, default='topology' Untyped OpenMM object to convert to Returns ------- open_mm_object : Untyped `topology` or `modeller` object """ openmm_top = app.Topology() # Get topology.positions into OpenMM form topology.positions.convert_to_units(u.nm) value = [i.value for i in topology.positions] openmm_pos = openmm_unit.Quantity(value=value, unit=openmm_unit.nanometer) # Adding a default chain and residue temporarily chain = openmm_top.addChain() residue = openmm_top.addResidue(name="RES", chain=chain) for site in topology.sites: openmm_top.addAtom(,, residue=residue ) # Set box box = box.lengths.convert_to_units(u.nanometer) lengths = box.lengths.value openmm_top.setUnitCellDimensions(lengths) # TODO: Figure out how to add residues # TODO: Convert connections to OpenMM Bonds if openmm_object == "topology": return openmm_top else: modeller = app.Modeller(openmm_top, openmm_pos) return modeller
def to_system( topology, nonbondedMethod=None, nonbondedCutoff=0.8 * u.nm, switchDistance=0.6 * u.nm, constraints=None, rigidWater=True, implicitSolvent=None, implicitSolventKappa=None, implicitSolventSaltConc=0.0 * u.Unit("mol/dm**3"), temperature=300 * u.Kelvin, soluteDielectric=1.0, solventDielectric=78, removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005, flexibleConstraints=True, verbose=False, splitDihedrals=False, ): """ Convert a typed topology object to a typed OpenMM System. See for more information. Parameters ---------- topology : `Topology` object, default=None An untyped topology object. nonbondedMethod : cutoff method, optional, default=None Cutoff method specified for OpenMM system. Options supported are 'NoCutoff', 'CutoffNonPeriodic', 'CutoffPeriodic', 'PME', or Ewald objects from nonbondedCutoff : unyt array or float, default=0.8*u.nm The nonbonded cutoff must either be a float or a unyt array. Float interpreted in units of nm. switchDistance : unyt array or float, default=0.6*u.nm The distance at which the switching function is turned on for van der waals interactions. This is ignored when no cutoff is used, and no switch is used if switchDistance is 0, negative, or greater than the cutoff. Float point interpreted in units of nm. constraints : 'None', 'app.HBonds', 'app.HAngles', or 'app.AllBonds' Type of constraints to add to the System (e.g., SHAKE). rigidWater : boolean, optional, default=True If True, water is kept rigid regardless of constraint values. False value is overriden if constraints is not None implicitSolvent : 'None', 'app.HCT', 'app.OBC1', 'app.OBC2', 'app.GBn', 'app.GBn2'. Default=None The Generalized Born implicit solvent model to use. implicitSolventKappa : 1/distance unyt array or float, default=None Debye kappa property related to modeling saltware conditions in GB. It should have units of 1/distance (interpreted as 1/nanometers if no units reported). A value of 'None' means that kappa will be calculated from implicitSolventSaltConc. implicitSolventSaltConc : amount/volume unyt array or float, default=0 moles/Liter (moles/dm^3) if implicitSolventKappa is 'None', the kappa will be computed from salt concentration. Units should be compatible with mol/L. temperature : temperature unyt array or flow, default=300*u.K This is only used to compute kappa from implicitySolventSaltConc. If not unit given, temperature will be interpreted in units of Kelvin. soluteDielectric : float, default=1.0 The dielectric constant of protein interior used in GB. solventDielectric : float, default=78.5 The dielectric constant of water used in GB useSASA : boolean, default=False If True, use the ACE non-polar solvation model. Otherwise, no SASA-based nonpolar solvation model is used. removeCMMotion : boolean, default=True If True, the center-of-mass motion will be removed periodically during the simulation. If False, it will not. hydrogenMass : mass unyt array or float, default=None If not None, hydrogen masses will be changed to this mass and the difference subtracted from the attached heavy atom (hydrogen mass repartitioning). ewaldErrorTolerance : float, default=0.0005 When using PME or Ewald, the Ewald parameters will be calculated from this value. flexibleConstraints : boolean, optional, default=True If False, the energies and forces from the constrained degrees of freedom will NOT be computed. If True, they will but those degrees of freedom will *still* be constrained). verbose : boolean, optional, default=False If True, the progress of this subroutine will be printed to stdout. splitDihedrals : boolean, optional, default=False If True, the dihedrals will be split into two forces -- propers and impropers. This is primarily useful for debugging torsion parameter assignments. Returns ------- openmm_system : A typed OpenMM System object """ # TODO: Everything