Getting started guide

There is so much to say about molecular dynamics (MD) simulations that at the beginning it may seem a bit daunting. Below we list a few resources that may be useful to step into the world of MD.

1. Some useful books and reviews

   • Frenkel & Smit, Understanding Molecular Simulation, From Algorithms to Applications (2nd. Ed., 2001).
   • Allen & Tildesley, Computer Simulation of Liquids (2nd. Ed., 2017). See the companion repository.
   • Best Practices for Foundations in Molecular Simulations, Braun et al. Living J. Comp. Mol. Sci. (2019). DOI: 10.33011/livecoms.1.1.5957

2. How to use the Gromacs software package

   • Justin Lemkul's tutorials page: http://www.mdtutorials.com/

3. Analysis packages:

   • The MDtraj Python library: http://mdtraj.org

4. Coarse grained models

   • SMOG: This webtool allows for you to generate parameters to run coarse-grained simulations in Gromacs with the famous Clementi model.

5. Visualization

   • VMD: An incredible program for visualizing your MD simulation data. You can find a tutorial here.