Welcome to ensemble_md’s documentation!

ensemble_md is a Python package providing methods for running GROMACS simulation ensembles, including ensemble of expanded ensemble and ensemble of alchemical metadynamics. The former is our main focus in our current phase, while the latter will be under development in the future.

Getting started:

• 1. Introduction
• 2. Installation
  • 2.1. Requirements
  • 2.2. Installation via pip
  • 2.3. Installation from source
• 3. Testing
  • 3.1. Tests for the functions that do not use MPI
  • 3.2. Tests for the functions that use MPI

Theory:

• 1. Basic idea
• 2. REXEE configuration
• 3. State transitions in REXEE simulations
• 4. Proposal schemes
  • 4.1. Single exchange proposal scheme
  • 4.2. Neighbor exchange proposal scheme
  • 4.3. Exhaustive exchange proposal scheme
• 5. Correction schemes
  • 5.1. Weight combination
  • 5.2. Weight correction
  • 5.3. Histogram correction
  • 5.3. Our experience with the correction schemes
• 6. Free energy calculations

Launching REXEE simulations:

• 1. Command-line interface (CLI)
  • 1.1. CLI explore_REXEE
  • 1.2. CLI run_REXEE
  • 1.3. CLI analyze_REXEE
• 2. Implemented workflow
  • Step 1: Set up parameters
  • Step 2: Run the 1st iteration
  • Step 3: Set up the new iteration
  • Step 4: Run the new iteration
• 3. Input YAML parameters
  • 3.1. GROMACS executable
  • 3.2. Input files
  • 3.3. REXEE parameters
  • 3.4. Output settings
  • 3.5. Data analysis
  • 3.6. A template input YAML file
• 4. Input MDP parameters
• 5. Some rules of thumb

Tutorials:

• Tutorial 1: Launching a REXEE simulation
• Tutorial 2: Analyzing a REXEE simulation
• Tutorial 3: Multi-topology REXEE (MT-REXEE) simulations

API documentation:

• ensemble_md.replica_exchange_EE
  • ReplicaExchangeEE
• ensemble_md.analysis
  • ensemble_md.analysis.analyze_traj
  • ensemble_md.analysis.analyze_matrix
  • ensemble_md.analysis.analyze_free_energy
  • ensemble_md.analysis.synthesize_data
  • ensemble_md.analysis.clustering
  • ensemble_md.analysis.msm_analysis
• ensemble_md.utils
  • ensemble_md.utils.gmx_parser
  • ensemble_md.utils.utils
  • ensemble_md.utils.exceptions

References:

• References

Others

• Index