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. |