DesmondDMSFile¶
- class 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
Get the positions of each atom in the system
Get the provenance string of this system
Get the topology of the system
Get the positions of each atom in the system
setPositions
(positions)Update atomic positions in attached DMS files
setVelocities
(velocities)Update atomic velocities in attached DMS files
- 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