The adaptive-sampling Python Package

Welcome to the adaptive-sampling package documentation!

Contents:

• Introduction
  • The adaptive_sampling package
  • Warning
• Installation
  • Dependencies
• Basic usage
  • Molecular dynamics (MD) interfaces
  • Sampling tools
  • Exploration tools
• Sampling tools
  • The EnhancedSampling Base Class
  • (Well-tempered) metadynamics (WTM)
  • On-the-fly probability enhanced sampling (OPES)
  • Extended-system dynamics
  • Accelerated molecular dynamics (aMD)
• Collective Variables (CVs)
  • Common CVs
  • Path CVs (PCVs)
  • Machine Learning CVs (MLCVs):
  • The Modified Center-of-Excess Charge (mCEC):
  • Graph-based CVs (Graph-CVs):
• Exploration tools
• Processing tools
  • Extended-system dynamics
• Tutorials
  • Compute the alanine dipeptide [\(\Phi,\Psi\)] transition using OpenMM and OPES-eABF
  • Compute the alanine dipeptide [\(\Phi,\Psi\)] transition using OpenMM and OPES
• Code Documentation
  • The adaptive_sampling package
  • Sampling Algorithms
  • Processing Tools
  • Molecular Dynamics Interfaces
  • Collective Variables
• Scientific articles using the adaptive_sampling package