Package ffx.openmm
@ParametersAreNonnullByDefault
package ffx.openmm
The OpenMM package includes Java classes that are analogues of the OpenMM C++ API.
- Since:
- 1.0
- Author:
- Michael J. Schnieders
-
ClassesClassDescriptionThis class uses the Andersen method to maintain constant temperature.The ATMForce class implements the Alchemical Transfer Method (ATM) for OpenMM.Bonds are specified by pairs of integers (the atom indices).This is an Integrator which simulates a System using Brownian dynamics.This class implements an interaction between pairs of dihedral angles.This class prevents the center of mass of a System from drifting.This class allows you to use multiple integration algorithms within a single simulation, switching back and forth between them.A Context stores the complete state of a simulation.This is a TabulatedFunction that computes a continuous one dimensional function.This is a TabulatedFunction that computes a continuous two dimensional function.This is a TabulatedFunction that computes a continuous three dimensional function.This class implements interactions between sets of three particles that depend on the angle between them.This class implements bonded interactions between pairs of particles.This class is similar to CustomCompoundBondForce, but instead of applying forces between individual particles, it applies them between the centers of groups of particles.This class supports a wide variety of bonded interactions.This class supports energy functions that depend on collective variables.This class implements an "external" force on particles.This class implements complex, multiple stage nonbonded interactions between particles.This class supports a wide variety of energy functions used to represent hydrogen bonding.This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms.This class supports a wide variety of nonbonded N-particle interactions, where N is user specified.This class implements nonbonded interactions between particles.This class implements interactions between sets of four particles that depend on the torsion angle between them.This class computes an energy that depends only on the volume of the periodic box, or more generally on the box shape as specified by the elements of the box vectors.This is a TabulatedFunction that computes a discrete one dimensional function f(x).This is a TabulatedFunction that computes a discrete two dimensional function f(x,y).This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z).DoubleArray wrapper.Force objects apply forces to the particles in a System, or alter their behavior in other ways.This class implements the Gay-Berne anisotropic potential.This class implements an implicit solvation force using the GBSA-OBC model.This class implements an interaction between groups of three particles that varies harmonically with the angle between them.This class implements an interaction between pairs of particles that varies harmonically with the distance between them.Int Array.An Integrator defines a method for simulating a System by integrating the equations of motion.Int Set.This is an Integrator which simulates a System using Langevin dynamics.This is an Integrator which simulates a System using Langevin dynamics, with the LFMiddle discretization (J.This is a VirtualSite that computes the particle location based on a local coordinate system.A MinimizationReporter can be passed to LocalEnergyMinimizer::minimize() to provide periodic information on the progress of minimization, and to give you the chance to stop minimization early.This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure.This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure.This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure.This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure and surface tension on a membrane system.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.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.This is a VirtualSite that computes the particle location based on three other particles' locations.This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them.A Platform defines an implementation of all the kernels needed to perform some calculation.This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential.This is a force whose energy equals the root mean squared deviation (RMSD) between the current coordinates and a reference structure.A State object records a snapshot of the current state of a simulation at a point in time.String Array.This class represents a molecular system.A TabulatedFunction uses a set of tabulated values to define a mathematical function.This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations.This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations.This class implements a Langevin integrator with variable time stepping.This class implements a Verlet integrator with variable time stepping.Vec3 Array.Verlet Integrator.A VirtualSite describes the rules for computing a particle's position based on other particles.