DesmondDMSFile¶
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class
simtk.openmm.app.desmonddmsfile.
DesmondDMSFile
(file)¶ DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it
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__init__
(file)¶ Load a DMS file
Parameters: file (string) – the name of the file to load
Methods
__init__
(file)Load a DMS file close
()Close the SQL connection createSystem
([nonbondedMethod, ...])Construct an OpenMM System representing the topology described by this 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
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getTopology
()¶ Get the topology of the system
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getProvenance
()¶ Get the provenance string of this system
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createSystem
(nonbondedMethod=NoCutoff, nonbondedCutoff=Quantity(value=1.0, unit=nanometer), ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None)¶ 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, or PME.
- 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 or PME.
- 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.
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close
()¶ Close the SQL connection
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