PyRETIS 2

PyRETIS 2 implements interface-based path sampling methods, including transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), to compute quantitative rate constants and sample rare-event pathways in molecular dynamics simulations.

Key Features:

• Interface-Based Path Sampling: Employs interface-based path sampling methods such as transition interface sampling (TIS) to enable quantitative rate calculations.
• Replica Exchange Transition Interface Sampling (RETIS): Implements RETIS for replica-exchange sampling of path ensembles to improve sampling of rare events.
• Interoperability with MD Packages: Interfaces with molecular dynamics packages and supports both classical and ab initio MD simulations.
• Shooting Moves: Provides multiple shooting moves, including recently introduced new shooting moves, to enhance path sampling efficiency.
• Analysis Tools: Includes comprehensive analysis methods for examination and interpretation of path ensembles and rate calculations.
• Support for Interfaced Software: Supports a range of interfaced software for coupling path sampling to external simulation engines.

Scientific Applications:

• Computational chemistry and rare-event studies: Used to study rare events and compute rate constants in molecular systems.
• Enzyme reaction kinetics: Applied to quantify rates and mechanisms of enzyme reactions.
• Protein folding pathways: Used to sample folding and unfolding pathways and calculate folding rates.
• Ligand binding/unbinding kinetics: Applied to characterize ligand binding and unbinding kinetics and pathways.

Methodology:

Uses transition interface sampling (TIS), replica exchange transition interface sampling (RETIS), interface-based path sampling and multiple shooting moves, interfaces to external MD engines for classical and ab initio MD, and provides analysis of path ensembles and rate calculations.