OpenMM Namespace Reference

This file provides a variety of macros useful in test cases. More...

Classes
class	AndersenThermostat
	This class uses the Andersen method to maintain constant temperature. More...
class	BrownianIntegrator
	This is an Integrator which simulates a System using Brownian dynamics. More...
class	CMAPTorsionForce
	This class implements an interaction between pairs of dihedral angles. More...
class	CMMotionRemover
	This class prevents the center of mass of a System from drifting. More...
class	Context
	A Context stores the complete state of a simulation. More...
class	CustomAngleForce
	This class implements interactions between sets of three particles that depend on the angle between them. More...
class	CustomBondForce
	This class implements bonded interactions between pairs of particles. More...
class	CustomCompoundBondForce
	This class supports a wide variety of bonded interactions. More...
class	CustomExternalForce
	This class implements an "external" force on particles. More...
class	CustomGBForce
	This class implements complex, multiple stage nonbonded interactions between particles. More...
class	CustomHbondForce
	This class supports a wide variety of energy functions used to represent hydrogen bonding. More...
class	CustomIntegrator
	This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms. More...
class	CustomNonbondedForce
	This class implements nonbonded interactions between particles. More...
class	CustomTorsionForce
	This class implements interactions between sets of four particles that depend on the torsion angle between them. More...
class	Force
	Force objects apply forces to the particles in a System, or alter their behavior in other ways. More...
class	GBSAOBCForce
	This class implements an implicit solvation force using the GBSA-OBC model. More...
class	GBVIForce
	This class implements an implicit solvation force using the GB/VI model. More...
class	HarmonicAngleForce
	This class implements an interaction between groups of three particles that varies harmonically with the angle between them. More...
class	HarmonicBondForce
	This class implements an interaction between pairs of particles that varies harmonically with the distance between them. More...
class	Integrator
	An Integrator defines a method for simulating a System by integrating the equations of motion. More...
class	AndersenThermostatImpl
	This is the internal implementation of AndersenThermostat. More...
class	CMAPTorsionForceImpl
	This is the internal implementation of CMAPTorsionForce. More...
class	CMMotionRemoverImpl
	This is the internal implementation of CMMotionRemover. More...
class	ContextImpl
	This is the internal implementation of a Context. More...
class	CustomAngleForceImpl
	This is the internal implementation of CustomAngleForce. More...
class	CustomBondForceImpl
	This is the internal implementation of CustomBondForce. More...
class	CustomCompoundBondForceImpl
	This is the internal implementation of CustomCompoundBondForce. More...
class	CustomExternalForceImpl
	This is the internal implementation of CustomExternalForce. More...
class	CustomGBForceImpl
	This is the internal implementation of CustomGBForce. More...
class	CustomHbondForceImpl
	This is the internal implementation of CustomHbondForce. More...
class	CustomNonbondedForceImpl
	This is the internal implementation of CustomNonbondedForce. More...
class	CustomTorsionForceImpl
	This is the internal implementation of CustomTorsionForce. More...
class	ForceImpl
	A ForceImpl provides the internal implementation of a Force. More...
class	GBSAOBCForceImpl
	This is the internal implementation of GBSAOBCForce. More...
class	GBVIForceImpl
	This is the internal implementation of GBVIForce. More...
class	HarmonicAngleForceImpl
	This is the internal implementation of HarmonicAngleForce. More...
class	HarmonicBondForceImpl
	This is the internal implementation of HarmonicBondForce. More...
class	MonteCarloAnisotropicBarostatImpl
	This is the internal implementation of MonteCarloAnisotropicBarostat. More...
class	MonteCarloBarostatImpl
	This is the internal implementation of MonteCarloBarostat. More...
class	NonbondedForceImpl
	This is the internal implementation of NonbondedForce. More...
class	PeriodicTorsionForceImpl
	This is the internal implementation of PeriodicTorsionForce. More...
class	RBTorsionForceImpl
	This is the internal implementation of RBTorsionForce. More...
class	SplineFitter
	SplineFitter provides routines for performing cubic spline interpolation. More...
class	ThreadPool
	A ThreadPool creates a set of worker threads that can be used to execute tasks in parallel. More...
class	LangevinIntegrator
	This is an Integrator which simulates a System using Langevin dynamics. More...
class	LocalEnergyMinimizer
	Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy. More...
class	MonteCarloAnisotropicBarostat
	This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. More...
class	MonteCarloBarostat
	This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. More...
class	NonbondedForce
	This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions. More...
class	OpenMMException
	This class is used for all exceptions thrown by OpenMM. More...
class	PeriodicTorsionForce
	This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them. More...
class	RBTorsionForce
	This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential. More...
class	State
	A State object records a snapshot of the current state of a simulation at a point in time. More...
class	System
	This class represents a molecular system. More...
class	TabulatedFunction
	A TabulatedFunction uses a set of tabulated values to define a mathematical function. More...
class	Continuous1DFunction
	This is a TabulatedFunction that computes a continuous one dimensional function. More...
class	Continuous2DFunction
	This is a TabulatedFunction that computes a continuous two dimensional function. More...
class	Continuous3DFunction
	This is a TabulatedFunction that computes a continuous three dimensional function. More...
class	Discrete1DFunction
	This is a TabulatedFunction that computes a discrete one dimensional function f(x). More...
class	Discrete2DFunction
	This is a TabulatedFunction that computes a discrete two dimensional function f(x,y). More...
class	Discrete3DFunction
	This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z). More...
class	VariableLangevinIntegrator
	This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics. More...
class	VariableVerletIntegrator
	This is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm. More...
class	Vec3
	This class represents a three component vector. More...
class	VerletIntegrator
	This is an Integrator which simulates a System using the leap-frog Verlet algorithm. More...
class	VirtualSite
	A VirtualSite describes the rules for computing a particle's position based on other particles. More...
class	TwoParticleAverageSite
	This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations. More...
class	ThreeParticleAverageSite
	This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations. More...
class	OutOfPlaneSite
	This is a VirtualSite that computes the particle location based on three other particles' locations. More...
class	LocalCoordinatesSite
	This is a VirtualSite that uses the locations of three other particles to compute a local coordinate system, then places the virtual site at a fixed location in that coordinate system. More...
class	Kernel
	A Kernel encapsulates a particular implementation of a calculation that can be performed on the data in a Context. More...
class	KernelFactory
	A KernelFactory is an object that can create KernelImpls. More...
class	KernelImpl
	A KernelImpl defines the internal implementation of a Kernel object. More...
class	Platform
	A Platform defines an implementation of all the kernels needed to perform some calculation. More...
class	XmlSerializer
	XmlSerializer is used for serializing objects as XML, and for reconstructing them again. More...
class	DrudeForce
	This class implements forces that are specific to Drude oscillators. More...
class	DrudeLangevinIntegrator
	This Integrator simulates systems that include Drude particles. More...
class	DrudeSCFIntegrator
	This is a leap-frog Verlet Integrator that simulates systems with Drude particles. More...
class	DrudeForceImpl
	This is the internal implementation of DrudeForce. More...
class	RPMDIntegrator
	This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD). More...
class	AmoebaAngleForce
	This class implements an interaction between triplets of particles that varies with the angle between them. More...
class	AmoebaBondForce
	This class implements an interaction between pairs of particles that varies with the distance between them. More...
class	AmoebaGeneralizedKirkwoodForce
	This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model. More...
class	AmoebaInPlaneAngleForce
	This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles. More...
class	AmoebaMultipoleForce
	This class implements the Amoeba multipole interaction. More...
class	AmoebaOutOfPlaneBendForce
	This class implements the Amoeba out-of-plane bend interaction. More...
class	AmoebaPiTorsionForce
	This class implements the Amoeba pi-torsion interaction. More...
class	AmoebaStretchBendForce
	This class implements the Amoeba stretch-bend interaction. More...
class	AmoebaTorsionTorsionForce
	This class implements the Amoeba torsion-torsion interaction. More...
class	AmoebaVdwForce
	This class implements a buffered 14-7 potential used to model van der Waals forces. More...
class	AmoebaWcaDispersionForce
	This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model. More...
class	AmoebaAngleForceImpl
	This is the internal implementation of AmoebaAngleForce. More...
class	AmoebaBondForceImpl
	This is the internal implementation of AmoebaBondForce. More...
class	AmoebaGeneralizedKirkwoodForceImpl
	This is the internal implementation of AmoebaGeneralizedKirkwoodForce. More...
class	AmoebaInPlaneAngleForceImpl
	This is the internal implementation of AmoebaInPlaneAngleForce. More...
class	AmoebaMultipoleForceImpl
	This is the internal implementation of AmoebaMultipoleForce. More...
class	AmoebaOutOfPlaneBendForceImpl
	This is the internal implementation of AmoebaOutOfPlaneBendForce. More...
class	AmoebaPiTorsionForceImpl
	This is the internal implementation of AmoebaPiTorsionForce. More...
class	AmoebaStretchBendForceImpl
	This is the internal implementation of AmoebaStretchBendForce. More...
class	AmoebaTorsionTorsionForceImpl
	This is the internal implementation of AmoebaTorsionTorsionForce. More...
class	AmoebaVdwForceImpl
	This is the internal implementation of AmoebaVdwForce. More...
class	AmoebaWcaDispersionForceImpl
	This is the internal implementation of AmoebaWcaDispersionForce. More...

Typedefs
typedef std::vector < std::vector< std::vector < double > > >	TorsionTorsionGrid
typedef std::vector < std::vector< std::vector < float > > >	TorsionTorsionGridFloat

Functions
void OPENMM_EXPORT	throwException (const char *file, int line, const std::string &details)
template<class CHAR , class TRAITS >
std::basic_ostream< CHAR, TRAITS > &	operator<< (std::basic_ostream< CHAR, TRAITS > &o, const Vec3 &v)

Variables
class OPENMM_EXPORT	Force
class OPENMM_EXPORT	VirtualSite

Detailed Description

This file provides a variety of macros useful in test cases.

Typedef Documentation

typedef std::vector< std::vector< std::vector<double> > > TorsionTorsionGrid

typedef std::vector< std::vector< std::vector<float> > > TorsionTorsionGridFloat

Function Documentation

std::basic_ostream<CHAR,TRAITS>& OpenMM::operator<<	(	std::basic_ostream< CHAR, TRAITS > &	o,
		const Vec3 &	v
	)

void OPENMM_EXPORT OpenMM::throwException	(	const char *	file,
		int	line,
		const std::string &	details
	)

Variable Documentation

class OPENMM_EXPORT Force

class OPENMM_EXPORT VirtualSite