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