DesmondDMSFile

class simtk.openmm.app.desmonddmsfile.DesmondDMSFile(file, verbose=False)

DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it

__init__(file, verbose=False)

Load a DMS file

Parameters:

• file (list of strings (multiple files, each containing a molecule)) –
• or –
• file –
• name(s) of the file to load (the) –

Methods

__init__(file[, verbose])	Load a DMS file
close()	Close the SQL connections
createSystem([nonbondedMethod, …])	Construct an OpenMM System representing the topology described by this DMS file
getPositions()	Get the positions of each atom in the system
getProvenance()	Get the provenance string of this system
getTopology()	Get the topology of the system

getPositions()

Get the positions of each atom in the system

getVelocities()

Get the positions of each atom in the system

getTopology()

Get the topology of the system

getProvenance()

Get the provenance string of this system

setPositions(positions)

Update atomic positions in attached DMS files

setVelocities(velocities)

Update atomic velocities in attached DMS files

createSystem(nonbondedMethod=NoCutoff, nonbondedCutoff=Quantity(value=1.0, unit=nanometer), ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None, OPLS=False, implicitSolvent=None, AGBNPVersion=1)

Construct an OpenMM System representing the topology described by this DMS file

Parameters:

• nonbondedMethod (object=NoCutoff) – The method to use for nonbonded interactions. Allowed values are NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
• nonbondedCutoff (distance=1*nanometer) – The cutoff distance to use for nonbonded interactions
• ewaldErrorTolerance (float=0.0005) – The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
• removeCMMotion (boolean=True) – If true, a CMMotionRemover will be added to the System
• hydrogenMass (mass=None) – The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same.
• OPLS (boolean=False) – If True, forces OPLS combining rules
• implicitSolvent (string=None) – If not None, creates implicit solvent force of the given name Allowed values are: HCT and ‘AGBNP’ (the corresponding tables must be present in the DMS file)
• AGBNPVersion (int=1) – AGBNP implicit solvent version

close()

Close the SQL connections