RC-Finder-GPT: Uncover Reaction Coordinates for Rare Events
Your rare-event molecular dynamics assistant for mining simulation trajectories, proposing low-dimensional reaction coordinates (CVs) using ML, and validating them with biased simulations, inspired by Pratyush Tiwary.
Access RC-Finder-GPTWhat is RC-Finder-GPT?
RC-Finder-GPT is a specialized assistant for rare-event molecular dynamics, designed to help computational chemists and physicists discover and validate low-dimensional reaction coordinates (CVs). It mines simulation trajectories, employs contrastive or information-theoretic machine learning to propose optimal CVs, and guides users through their validation using biased simulations, enhancing the understanding of complex molecular transitions.
Accelerate Discovery of Molecular Mechanisms
Understand CV Discovery
Explains intuition behind various reaction coordinate discovery methods (e.g., spectral gap optimization vs. mutual information maximization) and compares approaches.
PLUMED Syntax & Testing
Helps users write PLUMED input syntax for testing a proposed CV and interpret resulting free energy or kinetics to evaluate its quality.
Automated CV Model Training
Loads MD trajectories and trains neural network-based CV models like VAMPnets or uses SGOOP to find candidate reaction coordinates.
Setup Biased Simulations
Outputs PLUMED biasing files for top CVs, enabling users to run metadynamics or umbrella sampling to validate and refine the coordinate.
Structured Analysis & Data
Provides Markdown analysis of CVs (e.g., "CV1 combines protein dihedrals..."), PLUMED inputs in code blocks, and CSV data for free energy profiles.
Confidential & Compliant
Removes proprietary molecular structures if confidential, anonymizes unpublished names, and cautions on export-controlled parameters.
Ready to Illuminate Complex Molecular Pathways?
Leverage RC-Finder-GPT to discover meaningful reaction coordinates, accelerate your rare-event sampling, and gain deeper insights into molecular dynamics.
Explore Reaction Coordinates