β’ Lipid bilayers - Part I: Self-assembly
Description: Basic tutorial on lipid bilayer self-assembly
β’ Lipid bilayers - Part II: Complex lipid mixtures
Description: Learn how to create complex lipid mixtures using Insane
β’ Proteins - Part I(a): Introduction
Description: A practical introduction to different structure bias models and their comparison
β’ Proteins - Part I(b): Using Martinize2
Description: Setup of Martini 3 Protein Structure Models
β’ Proteins - Part I(c): Evaluating Proteins Models
Description: Metrics to Compare Protein Structure Models
β’ Proteins - Part I(d): Intrinsically Disordered Regions
Description: Simulations of IDRs in Martini 3
β’ Proteins - Part I(e): Conclusions
Description: Additional Notes, Limitations, Summary, and Outlook
β’ Proteins - Part II(a): Setting Up Transmembrane Peptide Simulations
Description: Learn to build and simulate peptides embedded in lipid bilayers.
β’ Proteins - Part II(b): Protein complexes
Description: Advanced protein modeling applications: Protein complexes
β’ Parametrization of a new small molecule - (a) Classic Method
Description: Learn how to parametrize new molecules for Martini
β’ Parametrization of a new small molecule - (b) Semi-automated using Fast_Forward
Description: Learn how to parametrize new molecules for Martini in a semi-automated way using Fast_Forward
β’ Parametrization of a new small molecule - (c) Bartender for semi-empirical QM reference data
Description: Learn how to parametrize new molecules for Martini using semi-empirical QM
β’ Protein-small molecule binding
Description: Study protein-ligand interactions
β’ Reverse coarse-graining with Backward
Description: Convert Martini structures to atomistic resolution
β’ Backmapping systems with CG2AT
Description: Convert Martini structures to atomistic resolution with CG2AT
β’ Polyply: generating input parameters and coordinates
Description: Create complex molecular systems for Martini
β’ TS2CG as a membrane builder
Description: A tool for building complex membrane models
β’ Bentopy: from simple packing to building cellular models
Description: A tool for packing molecules in arbitrary volumes
β’ Running Martini simulation with ddcMD
Description: Learn how to use ddcMD for Martini simulations
β’ Titratable Martini for constant pH simulations
Description: Perform pH-dependent simulations with Martini
β’ Free energy techniques
Description: Introduction to free energy techniques with Gromacs
β’ ProLint2: Analysis of lipid-protein interactions
Description: Advanced analysis of lipid-protein interactions from Martini simulations
β’ Dual resolution membrane simulation
Description: Combine different resolution models for membrane simulations
β’ MDVContainment: Tutorial 1
Description: Learn how to use MDVContainment and hierarchical volumetric data analysis
To contribute with new tutorials, please get in touch with the Martini team through the Contacts Page or review the Contribution Guidelines to this web portal.