AndersenThermostat | This class uses the Andersen method to maintain constant temperature |
AndersenThermostatImpl | This is the internal implementation of AndersenThermostat |
BrownianIntegrator | This is an Integrator which simulates a System using Brownian dynamics |
CMAPTorsionForce | This class implements an interaction between pairs of dihedral angles |
CMAPTorsionForceImpl | This is the internal implementation of CMAPTorsionForce |
CMMotionRemover | This class prevents the center of mass of a System from drifting |
CMMotionRemoverImpl | This is the internal implementation of CMMotionRemover |
Context | A Context stores the complete state of a simulation |
ContextImpl | This is the internal implementation of a Context |
CustomAngleForce | This class implements interactions between sets of three particles that depend on the angle between them |
CustomAngleForceImpl | This is the internal implementation of CustomAngleForce |
CustomBondForce | This class implements bonded interactions between pairs of particles |
CustomBondForceImpl | This is the internal implementation of CustomBondForce |
CustomExternalForce | This class implements an "external" force on particles |
CustomExternalForceImpl | This is the internal implementation of CustomExternalForce |
CustomGBForce | This class implements complex, multiple stage nonbonded interactions between particles |
CustomGBForceImpl | This is the internal implementation of CustomGBForce |
CustomHbondForce | This class supports a wide variety of energy functions used to represent hydrogen bonding |
CustomHbondForceImpl | This is the internal implementation of CustomNonbondedForce |
CustomNonbondedForce | This class implements nonbonded interactions between particles |
CustomNonbondedForceImpl | This is the internal implementation of CustomNonbondedForce |
CustomTorsionForce | This class implements interactions between sets of four particles that depend on the torsion angle between them |
CustomTorsionForceImpl | This is the internal implementation of CustomTorsionForce |
Force | Force objects apply forces to the particles in a System, or alter their behavior in other ways |
ForceImpl | A ForceImpl provides the internal implementation of a Force |
GBSAOBCForce | This class implements an implicit solvation force using the GBSA-OBC model |
GBSAOBCForceImpl | This is the internal implementation of GBSAOBCForce |
GBVIForce | This class implements an implicit solvation force using the GB/VI model |
GBVIForceImpl | This is the internal implementation of GBVIForce |
HarmonicAngleForce | This class implements an interaction between groups of three particles that varies harmonically with the angle between them |
HarmonicAngleForceImpl | This is the internal implementation of HarmonicAngleForce |
HarmonicBondForce | This class implements an interaction between pairs of particles that varies harmonically with the distance between them |
HarmonicBondForceImpl | This is the internal implementation of HarmonicBondForce |
Integrator | An Integrator defines a method for simulating a System by integrating the equations of motion |
Kernel | A Kernel encapsulates a particular implementation of a calculation that can be performed on the data in a Context |
KernelFactory | A KernelFactory is an object that can create KernelImpls |
KernelImpl | A KernelImpl defines the internal implementation of a Kernel object |
LangevinIntegrator | This is an Integrator which simulates a System using Langevin dynamics |
LocalEnergyMinimizer | Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy |
MonteCarloBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure |
MonteCarloBarostatImpl | This is the internal implementation of MonteCarloBarostat |
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 |
NonbondedForceImpl | This is the internal implementation of NonbondedForce |
OpenMMException | This class is used for all exceptions thrown by OpenMM |
PeriodicTorsionForce | This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them |
PeriodicTorsionForceImpl | This is the internal implementation of PeriodicTorsionForce |
Platform | A Platform defines an implementation of all the kernels needed to perform some calculation |
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 |
RBTorsionForceImpl | This is the internal implementation of RBTorsionForce |
SplineFitter | SplineFitter provides routines for performing cubic spline interpolation |
State | A State object records a snapshot of the current state of a simulation at a point in time |
System | This class represents a molecular system |
VariableLangevinIntegrator | This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics |
VariableVerletIntegrator | This is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm |
Vec3 | This class represents a three component vector |
VerletIntegrator | This is an Integrator which simulates a System using the leap-frog Verlet algorithm |
XmlSerializer | XmlSerializer is used for serializing objects as XML, and for reconstructing them again |