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Optimization and Sampling

Local and Global Minimization, Dynamics, and Alchemical Free Energy Simulations.

Command Purpose
Anneal Run simulated annealing to optimize a structure.
Dynamics Run dynamics simulations in a variety of ensembles.
DynamicsOpenMM Run dynamics simulations in a variety of ensembles accelerated by OpenMM.
Histogram Examine a histogram produced by orthogonal space sampling.
ManyBody Globally optimize the side-chains of a protein.
Minimize Minimize a structure using a variety of force fields.
MinimizeOpenMM Minimize a structure using a variety of force fields accelerated by OpenMM.
Thermodynamics Compute free energy differences using orthogonal space sampling.