Examples

• Conveyor Belt Thermodynamic Integration with Ensembler
  • Loading Ensembler and necessary external packages
  • Interactive Example
  • Build a conveyor belt object
  • Start a conveyor belt simulation
  • Visualizations of the trajectories
  • Simple analysis of the conveyor belt simulation
• EDS Simulation
  • The Problem
  • The Reference Potential
  • Sampling the Enveloping Potential
  • Calculating Free Energies With EDS
  • Many States
  • Literature:
• Enhanced Sampling Simulations
  • with Ensembler
  • Loading Ensembler and necessary external packages
  • Enhanced Sampling Simulations in 1D
  • Enhanced sampling
  • 2D systems
• Free Energy Calculations
  • References:
  • Benchmarking parameters
  • The Test System: Setting up a System
  • The Analyctical Solution: Nice if there is one
  • Free Energy Pertubation - BAR/Zwanzig: a simplistic start
  • Coupling Methods
  • State Coupled - Enveloping Distribution Sampling (EDS)
  • Hybrid Methods - \(\lambda\)-EDS
  • Enhanced Sampling with system Coupling
  • Final Results