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  • Introduction
    • Github
    • Publication
    • Theory
  • Installation
    • Stable Releases
    • Source Installation
  • Modules
    • Moves
      • Move
      • RandomLigandRotationMove
      • MoveEngine
      • Under Development
    • Simulation
      • SystemFactory
      • SimulationFactory
      • BLUESSimulation
    • Integrators
    • Utilities
    • Reporters
    • Formats
  • Tutorial
    • Introduction to BLUES
    • Background
      • Coupling MD simulations with random NCMC moves for enhanced sampling of ligand binding modes via BLUES
    • YAML Configuration
      • Input/Output
        • Output files
        • Input files to generate the structure of your system
        • Restart files
      • System configuration
        • (Optional) Hydrogen mass repartitioning
        • (Optional) Alchemical system configuration
      • Simulation Configuration
        • NPT Simulation
        • (Optional) Additional relaxation steps in the NCMC simulation
        • (Optional) Platform Properties
      • Reporter Configuration
        • (Optional) Advanced options to the ``traj_netcdf`` reporter
    • Running a BLUES simulation
      • Selecting a move and initialize the move engine
      • Generating the Systems for openMM: ``SystemFactory``
        • (Optional) Applying restraints or freezing atoms
      • Generating the OpenMM Simulations: ``SimulationFactory``
      • Run the BLUES Simulation
blues
  • Docs »
  • Overview: module code

All modules for which code is available

  • blues.formats
  • blues.integrators
  • blues.moves
  • blues.reporters
  • blues.simulation
  • blues.utils

© Copyright 2018, Samuel C. Gill, Nathan M. Lim, Kalistyn Burley, David L. Mobley Revision d2ef3647.

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