ForceField Class Reference

A ForceField constructs OpenMM System objects based on a Topology. More...

List of all members.

Classes
class	_AtomTypeParameters
	## Inner class used to record parameter values for atom types.
class	_BondData
	## Inner class used to encapsulate data about a bond.
class	_SystemData
	## Inner class used to encapsulate data about the system being created.
class	_TemplateAtomData
	## Inner class used to encapsulate data about an atom in a residue template definition.
class	_TemplateData
	## Inner class used to encapsulate data about a residue template definition.
class	_VirtualSiteData
	## Inner class used to encapsulate data about a virtual site.
Public Member Functions
def	__init__
	Load one or more XML files and create a ForceField object based on them.
def	loadFile
	Load an XML file and add the definitions from it to this FieldField.
def	getGenerators
	Get the list of all registered generators.
def	registerGenerator
	Register a new generator.
def	registerAtomType
	Register a new atom type.
def	registerResidueTemplate
	Register a new residue template.
def	registerScript
	Register a new script to be executed after building the System.
def	createSystem
	Construct an OpenMM System representing a Topology with this force field.

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Detailed Description

A ForceField constructs OpenMM System objects based on a Topology.

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Constructor & Destructor Documentation

def __init__	(		self,
			files
	)

Load one or more XML files and create a ForceField object based on them.

Parameters:

files

(list) A list of XML files defining the force field. Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory (for built in force fields), or an open file-like object with a read() method from which the forcefield XML data can be loaded.

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Member Function Documentation

def createSystem	(		self,
			topology,
			nonbondedMethod = NoCutoff,
			nonbondedCutoff = 1.0*unit.nanometer,
			constraints = None,
			rigidWater = True,
			removeCMMotion = True,
			hydrogenMass = None,
			args
	)

Construct an OpenMM System representing a Topology with this force field.

Parameters:

topology	(Topology) The Topology for which to create a System
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 and 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
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.
args	() Arbitrary additional keyword arguments may also be specified. This allows extra parameters to be specified that are specific to particular force fields.

Returns:

(system) the newly created System

def getGenerators

(

self

)

Get the list of all registered generators.

def loadFile	(		self,
			file
	)

Load an XML file and add the definitions from it to this FieldField.

Parameters:

file

(string or file) An XML file containing force field definitions. It may be either an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory (for built in force fields), or an open file-like object with a read() method from which the forcefield XML data can be loaded.

def registerAtomType	(		self,
			parameters
	)

Register a new atom type.

def registerGenerator	(		self,
			generator
	)

Register a new generator.

def registerResidueTemplate	(		self,
			template
	)

Register a new residue template.

def registerScript	(		self,
			script
	)

Register a new script to be executed after building the System.

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The documentation for this class was generated from the following file:

• forcefield.py