blues
stable
Introduction
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Publication
Theory
Installation
Stable Releases
Development Builds
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
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