Simulation provides a simplified API for running simulations with OpenMM and reporting results. More...

Inheritance diagram for Simulation:

Public Member Functions
def	__init__
	Create a Simulation. More...

def	minimizeEnergy
	Perform a local energy minimization on the system. More...

def	step
	Advance the simulation by integrating a specified number of time steps. More...

Public Attributes
	topology
	The Topology describing the system being simulated. More...

	system
	The System being simulated. More...

	integrator
	The Integrator used to advance the simulation. More...

	currentStep
	The index of the current time step. More...

	reporters
	A list of reporters to invoke during the simulation. More...

	context
	The Context containing the current state of the simulation. More...

Detailed Description

Simulation provides a simplified API for running simulations with OpenMM and reporting results.

A Simulation ties together various objects used for running a simulation: a Topology, System, Integrator, and Context. To use it, you provide the Topology, System, and Integrator, and it creates the Context automatically.

Simulation also maintains a list of "reporter" objects that record or analyze data as the simulation runs, such as writing coordinates to files or displaying structures on the screen. For example, the following line will cause a file called "output.pdb" to be created, and a structure written to it every 1000 time steps:

simulation.reporters.append(PDBReporter('output.pdb', 1000))

Constructor & Destructor Documentation

def __init__	(	self,
		topology,
		system,
		integrator,
		platform = `None`,
		platformProperties = `None`
	)

Create a Simulation.

Parameters

topology	(Topology) A Topology describing the the system to simulate
system	(System) The OpenMM System object to simulate
integrator	(Integrator) The OpenMM Integrator to use for simulating the System
platform	(Platform=None) If not None, the OpenMM Platform to use
platformProperties	(map=None) If not None, a set of platform-specific properties to pass to the Context's constructor

Member Function Documentation

def minimizeEnergy	(	self,
		tolerance = `1*unit.kilojoule/unit.mole`,
		maxIterations = `0`
	)

Perform a local energy minimization on the system.

Parameters

tolerance	(energy=1*kilojoule/mole) The energy tolerance to which the system should be minimized
maxIterations	(int=0) The maximum number of iterations to perform. If this is 0, minimization is continued until the results converge without regard to how many iterations it takes.

References Simulation.context.