Package ffx.potential
@ParametersAreNonnullByDefault
package ffx.potential
The Potential package implements molecular mechanics force fields with shared memory Parallel
Java and via OpenMM.
- Since:
- 1.0
- Author:
- Michael J. Schnieders
-
ClassDescriptionThe AssemblyState class stores the chemical and coordinate state of a Molecular Assembly.Compute the potential energy and derivatives for a dual-topology system.Compute the potential energy and derivatives of a molecular system described by a force field.The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and WaterPlatform describes a set of force field implementations that include a pure Java reference implementation (FFX), and two OpenMM implementations (OMM_CUDA and OMM_REF are supported)Implements an error-canceling quad topology, where two large dual-topology simulation legs are run simultaneously to arrive at a small sum.The Renderer class attempts to maximize throughput of graphics operations on MolecularAssembly instances.The current state of the molecular dynamics simulation.A record class to hold the state of a system.The Utilities class provides methods to locate functional units of an organic system.An enumeration of recognized file types.An enumeration of recognized organic polymers.This class computes the energy and Cartesian coordinate gradient, plus finite difference derivatives of lattice parameters.