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Advances in Molecular Modelling Workshop 2024

Mastering Parametrization in Martini 3: Tips and Tricks for Small Molecules and Lipids

This repository contains two tutorials designed for the Advances in Molecular Modeling Workshop hosted at the Niels Bohr Institute, University of Copenhagen. These sessions will be held on:

Date: December 9–10, 2024
Location: Auditorium A (Niels Bohr Institute, University of Copenhagen)

Workshop Session Details

Title: Workshop: Mastering Parametrization in Martini 3: Tips and Tricks for Small Molecules and Lipids
Speaker: Dr. Paulo Cesar Telles de Souza (ENS de Lyon, CNRS, France)

Tutorials Overview

These tutorials will guide participants through advanced Martini 3 parametrization techniques, focusing on:

  1. Tutorial 1: Parametrization of small molecules (Adapted from here)

    • Generate atomistic reference data;
    • Atom-to-bead mapping;
    • Generate target CG distributions from the CG mapped trajectory;
    • Optimize CG bonded parameters.

  2. Tutorial 2: Complex lipid mixtures and assembling a lipid from known fragments (Adapted from here)

    • Buiding membranes;
    • Simulating complex lipid mixtures;
    • Designing a New Lipid Based on a Small Fragment.

Additional Resources

Note: These tutorials are prepared specifically for the workshop participants and are meant for educational purposes. Ensure you cite the Martini developers and related work appropriately in your research.