Optimization and Sampling Commands

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

Command	Purpose
Anneal	The Anneal command runs simulated annealing to optimize a structure.
BAR	The BAR command evaluates a free energy difference using the Bennett Acceptance Ratio algorithm based on archives of snapshots.
Cluster	The Cluster command clusters structures utilizing RMSD.
Dynamics	The Dynamics command implements molecular and stochastic dynamics algorithms.
ForEachFile	The ForEachFile command runs another command (i.e., Energy or Minimize) on a series of files with support for MPI parallelization across nodes.
Histogram	The Histogram command prints out an Orthogonal Space Tempering histogram using an input structure and histogram (*.his) file.
ManyBody	The ManyBody command performs a discrete optimization using a many-body energy expansion and elimination expressions.
Minimize	The Minimize command uses a limited-memory BFGS algorithm to minimize the energy of a molecular system.
MinimizeCrystals	The MinimizeCrystals command uses a limited-memory BFGS algorithm to minimize the energy of a crystal, including both coordinates and/or unit cell parameters.
MinimizeOpenMM	The Minimize command uses an OpenMM accelerated L-BFGS algorithm to minimize the energy of a molecular system.
MutatePDB	The MutatePDB command mutates a residue of a PDB file.
Scheduler	The Scheduler command runs a Parallel Java job scheduler on a cluster with multiple nodes.
SortArc	The SortArc command sorts archive file snapshots from Monte Carlo Thermodynamics jobs by lambda value.
Superpose	The Superpose command superposes molecules form an ARC or multiple model PDB file (all v. all or one v. all) or between two PDB/XYZ files.
SuperposeCrystals	The SuperposeCrystals command quantifies the similarity of input crystals based on a novel progressive alignment approach.
Thermodynamics	The Thermodynamics command computes free energy differences using orthogonal space tempering or via windowed approaches.
TorsionScan	The TorsionScan command enumerates conformations of a molecule using torsional scans around rotatable bonds.