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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.