Library Layer¶
Core Objects¶
This class represents a molecular system. |
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A Context stores the complete state of a simulation. |
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A Platform defines an implementation of all the kernels needed to perform some calculation. |
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A State object records a snapshot of the current state of a simulation at a point in time. |
Forces¶
This class implements an interaction between triplets of particles that varies with the angle between them. |
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This class implements an interaction between pairs of particles that varies with the distance between them. |
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This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model. |
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This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles. |
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This class implements the Amoeba multipole interaction. |
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This class implements the Amoeba out-of-plane bend interaction. |
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This class implements the Amoeba pi-torsion interaction. |
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This class implements the Amoeba stretch-bend interaction. |
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This class implements the Amoeba torsion-torsion interaction. |
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This class models van der Waals forces in the AMOEBA force field. |
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This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model. |
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This class uses the Andersen method to maintain constant temperature. |
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This class implements an interaction between pairs of dihedral angles. |
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This class prevents the center of mass of a System from drifting. |
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This class implements interactions between sets of three particles that depend on the angle between them. |
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This class implements bonded interactions between pairs of particles. |
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This class supports energy functions that depend on collective variables. |
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This class is similar to CustomCompoundBondForce, but instead of applying forces between individual particles, it applies them between the centers of groups of particles. |
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This class supports a wide variety of bonded interactions. |
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This class implements an “external” force on particles. |
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This class implements complex, multiple stage nonbonded interactions between particles. |
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This class supports a wide variety of energy functions used to represent hydrogen bonding. |
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This class supports a wide variety of nonbonded N-particle interactions, where N is user specified. |
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This class implements nonbonded interactions between particles. |
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This class implements interactions between sets of four particles that depend on the torsion angle between them. |
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This class implements forces that are specific to Drude oscillators. |
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Force objects apply forces to the particles in a System, or alter their behavior in other ways. |
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This class implements an implicit solvation force using the GBSA-OBC model. |
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This class implements the Gay-Berne anisotropic potential. |
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This class implements an interaction between groups of three particles that varies harmonically with the angle between them. |
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This class implements an interaction between pairs of particles that varies harmonically with the distance between them. |
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This class implements all nonbonded interactions in the HIPPO force field: electrostatics, induction, charge transfer, dispersion, and repulsion. |
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This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. |
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This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. |
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This is a Monte Carlo barostat designed specifically for membrane simulations. |
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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. |
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This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them. |
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This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential. |
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This is a force whose energy equals the root mean squared deviation (RMSD) between the current coordinates and a reference structure. |
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This class is very similar to MonteCarloBarostat, but it is specifically designed for use with RPMDIntegrator. |
Integrators¶
AMDForceGroupIntegrator implements a single boost aMD integration algorithm. |
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AMDIntegrator implements the aMD integration algorithm. |
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This is an Integrator which simulates a System using Brownian dynamics. |
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This class allows you to use multiple integration algorithms within a single simulation, switching back and forth between them. |
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This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms. |
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A base class to encapsulate features common to Drude integrators. |
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This Integrator simulates systems that include Drude particles. |
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This Integrator simulates systems that include Drude particles. |
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This is a leap-frog Verlet Integrator that simulates systems with Drude particles. |
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DualAMDIntegrator implements a dual boost aMD integration algorithm. |
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An Integrator defines a method for simulating a System by integrating the equations of motion. |
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This is an Integrator which simulates a System using Langevin dynamics. |
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This is an Integrator which simulates a System using Langevin dynamics, with the LFMiddle discretization (J. |
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MTSIntegrator implements the rRESPA multiple time step integration algorithm. |
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MTSLangevinIntegrator implements the BAOAB-RESPA multiple time step algorithm for constant temperature dynamics. |
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This is an Integrator which simulates a System using one or more Nose Hoover chain thermostats, using the “middle” leapfrog propagation algorithm described in J. |
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This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD). |
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This is an error controlled, variable time step Integrator that simulates a System using Langevin dynamics. |
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This is an error controlled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm. |
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This is an Integrator which simulates a System using the leap-frog Verlet algorithm. |
Extras¶
This is a TabulatedFunction that computes a continuous one dimensional function. |
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This is a TabulatedFunction that computes a continuous two dimensional function. |
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This is a TabulatedFunction that computes a continuous three dimensional function. |
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This is a TabulatedFunction that computes a discrete one dimensional function f(x). |
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This is a TabulatedFunction that computes a discrete two dimensional function f(x,y). |
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This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z). |
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This is a VirtualSite that uses the locations of several other particles to compute a local coordinate system, then places the virtual site at a fixed location in that coordinate system. |
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Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy. |
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This class defines a chain of Nose-Hoover particles to be used as a heat bath to scale the velocities of a collection of particles subject to thermostating. |
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This is the class used for all exceptions thrown by the C++ library. |
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This is a VirtualSite that computes the particle location based on three other particles’ locations. |
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A SerializationNode stores information about an object during serialization or deserialization. |
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A SerializationProxy is an object that knows how to serialize and deserialize objects of a particular type. |
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A TabulatedFunction uses a set of tabulated values to define a mathematical function. |
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This is a VirtualSite that computes the particle location as a weighted average of three other particle’s locations. |
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This is a VirtualSite that computes the particle location as a weighted average of two other particle’s locations. |
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Vec3 is a 3-element tuple that supports many math operations. |
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A VirtualSite describes the rules for computing a particle’s position based on other particles. |
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XmlSerializer is used for serializing objects as XML, and for reconstructing them again. |