ensemble_md
stable

Getting started:

  • 1. Introduction
  • 2. Installation
  • 3. Testing

Theory:

  • 1. Basic idea
  • 2. REXEE configuration
  • 3. State transitions in REXEE simulations
  • 4. Proposal schemes
  • 5. Correction schemes
  • 6. Free energy calculations

Launching REXEE simulations:

  • 1. Command-line interface (CLI)
  • 2. Implemented workflow
  • 3. Input YAML parameters
  • 4. Input MDP parameters
  • 5. Some rules of thumb

Tutorials:

  • Tutorial 1: Standard REXEE simulations
  • Tutorial 2: Multi-topology REXEE (MT-REXEE) simulations

API documentation:

  • ensemble_md.replica_exchange_EE
  • ensemble_md.analysis
  • ensemble_md.utils

Resources:

  • External tutorials
  • References
ensemble_md
  • Overview: module code

All modules for which code is available

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

© Copyright 2022, Wei-Tse Hsu. Project structure based on the Computational Molecular Science Python Cookiecutter version 1.6. Revision 5357b8c3.

Built with Sphinx using a theme provided by Read the Docs.