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  • News

    Select a news topic from the list below, then select a news article to read.

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    • Latest

      The latest news on Martini!
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    • Articles

      Recently published articles on Martini.
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      43
  • Martini tutorials

    The tutorial exercises described here aim to help you familiarize yourself with some of the basic and more advanced aspects of using GROMACS to perform coarse-grained simulations. The main focus is on the semi-empirical MARTINI model. Familiarity with GROMACS is assumed; for explanation of how to work with GROMACS and the specification of force field and run parameters we refer to the GROMACS user manual and web-pages (www.gromacs.org). There is an excellent GROMACS tutorial available at: http://md.chem.rug.nl/~mdcourse/index.html

    Are you wondering where to start? Try our Martini flowchart!

    The current tutorial follows a historical track, starting with the MARTINI model for lipids. It then goes on to describe how to set up simulations with proteins (and peptides), combine an elastic network with MARTINI (ElNeDyn), and ends with more advanced topics, like reverse mapping (i.e. fine graining from a coarse-grained structure), polarizable water and visualizing coarse grain structures. The material can be covered in as much time as you like, and the speed at which you go through this material depends on the computational facilities available, your GROMACS skills, and the time you take to consider what you’re doing. The set-up is modular, however, and depending on you particular interest, you may change the order of the exercises. You could either leave long runs overnight to return to them the next day, or use ”pre-prepared” intermediate and result files that can be downloaded.

    These tutorials were originally written for the MARTINI winterschool 2008 in Helsinki by Lars Schäfer, Andrzej Rzepiela, and Martti Louhivuori, subsequently updated by Clement Arnarez, Alex de Vries and Djurre de Jong for the CECAM Coarse grain workshop 2011 and further updated by Clement Arnarez, Helgi Ingólfsson, Manuel Nuno Melo and Jaakko Uusitalo for the 2nd Molecular Simulation Summer School at the University of Calgary.

     

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  • Downloads

    One of the strong assets of the Martini force field is it's easy availability. Here we provide parameter files, example run parameters and example topology files in Gromacs format. Note that Martini has also be implemented in other MD-packages, such as VMD.

    In addition we provide specific run parameters, starting structures and topology files from (published) example applications. And last but not least there is a collections of scripts and programs that over the years have been developed in our group and simplify the setup and/or analysis of Martini systems.


     

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  • About

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    4
  • Martini 2 Tutorials

    This is the page for Martini 2 tutorials.

     

    The tutorial exercises described here aim to help you familiarize yourself with some of the basic and more advanced aspects of using GROMACS to perform coarse-grained simulations. The main focus is on the semi-empirical MARTINI model. Familiarity with GROMACS is assumed; for explanation of how to work with GROMACS and the specification of force field and run parameters we refer to the GROMACS user manual and web-pages (www.gromacs.org). There is an excellent GROMACS tutorial taking you through atomistic simulation of a small peptide, available at: http://md.chem.rug.nl/~mdcourse/pepmd/index.html

    The tutorials are currently not presented in a particular logical order. However, beginners are advised to   start with the MARTINI model for LIPIDS, because in this tutorial both gromacs commands and Martini files are shown and discussed in most detail. A logical next step is to discover how to set up simulations with PROTEINS (and peptides) from a PDB file, combine an elastic network with MARTINI, or use the alternative ElNeDyn model. The protein tutorial also covers more advanced topics, like embedding peptides in a lipid bilayer, and reverse mapping (i.e. fine graining from a coarse-grained structure). Further experience with the protein model can be gained with the High throughput peptide self assembly tutorial, which also shows how many tasks can be automated by using clever scripting. Next in the MARTINI zoo are DNA and RNA, which also introduces third-party websites for building initial structures and a DNA-protein complex. Moving away from biomolecules, the POLYMERS tutorial lets you explore refining a model for PEO/PEG, discussing tools and strategies to develop your own MARTINI model(s); PARAMETRIZING your own molecule also covers this topic, but in a more general way. Finally, there is cutting-edge technology in the HYBRID model using virtual sites. 

     

    The material can be covered in as much time as you like, and the speed at which you go through this material depends on the computational facilities available, your GROMACS skills, and the time you take to consider what you’re doing. The set-up is modular, however, and depending on you particular interest, you may change the order of the exercises. You could either leave long runs overnight to return to them the next day, or use ”pre-prepared” intermediate and result files that can be downloaded.

    These tutorials were originally written for the MARTINI winterschool 2008 in Helsinki by Lars Schäfer, Andrzej Rzepiela, and Martti Louhivuori, subsequently updated by Clement Arnarez, Alex de Vries and Djurre de Jong for the CECAM Coarse grain workshop 2011 and further updated by Clement Arnarez, Helgi Ingólfsson, Manuel Nuno Melo and Jaakko Uusitalo for the 2nd Molecular Simulation Summer School at the University of Calgary. Further updates and contributions were added for the Martini Workshops 2015 and 2017, adding to the contributors Pim Frederix and Ignacio Faustino.  

     

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  • Martini 3 Tutorials

    The tutorials described here aim to help you familiarize yourself with some of the basic and more advanced aspects of using GROMACS to perform Martini 3.0 simulations. This page is currently under expansion. More tutorials are available for Martini 2: http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5
    The Martini 3.0 tutorials were written by Riccardo Alessandri, Juan Carlos Ramírez Palacios, Paulo C. T. Souza, and Sebastian Thallmair.
    Note: This tutorial, now based on the Martini 3 open-beta version (v.3.0.b.3.2), will be updated as soon as the final parameters of Martini 3 are available (the paper is under review right now).
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  • 2021 Martini online workshop

    Welcome to the 2021 Martini online workshop!

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    • Lectures

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    • Tutorials

      Welcome to the 2021 Martini online workshop tutorial page!

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      14