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

  3. Analysis packages:

  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.