Hands-on tutorial materials

• Coarse Graining Workshop 2009 Exercise Instructions

This pdf-file contains the instructions to do the hands-on exercises for Wednesday-Friday.

• CG-2009 Lipid Tutorial hands-on files 

A gzipped tar file containing the Coarse Graining Workshop 2009 lipid tutorial hands-on exercise materials (Wed).

• CG-2009 Coarse Graining Methane in Water Tutorial hands-on files 

This tar-file contains the files needed to run the hands-on exercises to create a coarse grained potential for methane in water (Fri).

• CG-2009 Reverse Mapping Tutorial hands-on files

This gzipped tar file contains the input files needed to run the reverse mapping tutorial. Note that you also need a special version of Gromacs (found here, too) to do the job (Thu).

• CG-2009 Reverse Mapping Capable version of Gromacs

You can use this version of Gromacs to run the reverse mapping tutorial. Note, that you need to compile it (Thu).

• CG-2009 Protein Tutorial hands-on files

This gzipped tar file contains the input files for the protein tutorial (Thu).

• Sample output from above tutorials

This link leads to a page where output from different tutorials are available.

Lecture slides in pdf-format

• Alex de Vires: Lecture Slides from Wednesday
• Alex de Vries: Lecture Slides on CG-model Validation
• SJ Marrink: Philosophy of the MARTINI Model - with Lipids & Applications
• SJ Marrink: MARTINI Applications for Proteins and Peptides
• SJ Marrink: MARTINI Model for Carbohydrates & New Ideas. View for How to Develop MARTINI Force Fields for Your Own Molecule
• Berk Hess: Introduction to GROMACS and its Recent Development
• Berk Hess: Coarse Graining Through PMF's with Theory and Applications
• Luca Monticelli: MARTINI Model for Proteins
• Luca Monticelli: MARTINI Applications for Peptides & Nanomaterials

Contributed talk slides from Friday

• Godehard Sutmann: Multi-Particle Collision Dynamics on Massively Parallel Computers
• Samuli Ollila: 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes
• Teemu Murtola: Improved Analysis of Gromacs trajectories - Dynamic Selections and Library Functions 
• Sergio Pantano: A Transferable, Accurate and Unbiased CG Model for Simulating RNA
• Alexander Lyubartsev: Systematic Coarse-Graining of Molecular Models by Inverse Monte Carlo
• Andrea Danani: Multiscale Modeling Applied to Polymer-Clay Nanocomposites
• Outi Lampela: Coarse-grained Calculation of the Molecular Polarizability of Proteins