AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it. More...
Public Member Functions | |
def | __init__ |
Load a prmtop file. | |
def | createSystem |
Construct an OpenMM System representing the topology described by this prmtop file. | |
Public Attributes | |
topology | |
The Topology read from the prmtop file. |
AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it.
def __init__ | ( | self, | ||
file | ||||
) |
Load a prmtop file.
def createSystem | ( | self, | ||
nonbondedMethod = ff.NoCutoff , |
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nonbondedCutoff = 1.0*unit.nanometer , |
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constraints = None , |
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rigidWater = True , |
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implicitSolvent = None , |
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soluteDielectric = 1.0 , |
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solventDielectric = 78.5 , |
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removeCMMotion = True | ||||
) |
Construct an OpenMM System representing the topology described by this prmtop file.
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 | |
constraints | (object=None) Specifies which bonds angles should be implemented with constraints. Allowed values are None, HBonds, AllBonds, or HAngles. | |
rigidWater | (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument | |
implicitSolvent | (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, or GBn. | |
soluteDielectric | (float=1.0) The solute dielectric constant to use in the implicit solvent model. | |
solventDielectric | (float=78.5) The solvent dielectric constant to use in the implicit solvent model. | |
removeCMMotion | (boolean=True) If true, a CMMotionRemover will be added to the System |
The Topology read from the prmtop file.