Package ffx.algorithms.commands.test
package ffx.algorithms.commands.test
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ClassesClassDescriptionThe ApplyTorsions script is used to apply a custom set of torsions to a side chain.CoformerBindingSearch is a Groovy script that generates a set of molecular orientations in vacuum and calculates the energy of each conformation.The CreateRotamers script creates a set of conformation dependent rotamers.The CrystalSearch script searches for minimum energy polymorphs for a given space group.The FindRestraints script identifies guest molecule atoms that should be restrained based on their proximity to specific atoms in a host molecule.The Freefix script calculates analytical free energy, entropy, and enthalpy corrections for flat-bottom harmonic restraints with inner and outer radii.The IdentifyRotamers script attempts to identify which rotamer each Residue in the system is in.The ManyBodyPhScan script runs a pH scan with ManyBody optimization by executing another FFXScript multiple times across a pH range.The MinimizePh command uses a limited-memory BFGS algorithm to minimize the energy of a CpHMD molecular system.The MostBar script uses a single set of archive file(s) from a Metropolized Orthogonal Space Tempering run to evaluate free energy via the Bennett Acceptance Ratio
Usage:
ffxc test.MostBar [options] <structures1>OSTGradient tests the Orthogonal Space Tempering Potential.The PhDynamics command implements constant pH molecular dynamics.Use the Rao-Blackwell Estimator to estimate a free energy difference of protonation for a CpHMD system.The RepexThermo command uses the Orthogonal Space Tempering with histogram replica exchange to estimate a free energy difference.The SortXPH command unwinds .ARC files from CpHMD runs.WeightedEnsemble
Usage: Accelerated Sampling with Weighted Ensemble
ffxc test.WeightedEnsemble [options] <filename> [file2