GROMACS (GROningen MAchine for Simulations) is an efficient, versatile, well-documented, and free software for molecular dynamics simulations. We use it extensively in our research.
The Gromacs website is here, with excellent documentation for how to use the simulation platform and associated analysis tools. The manual in PDF form (version 4 here, version 5 here) is well worth reading.
Gromacs tutorial
Our group has prepared an extensive tutorial for new users, that begins with the basic structure of a simulation, and continues with more advanced techniques not extensively documented in the Gromacs manuals. The various input files needed to run the examples in the tutorial are here:
Gromacs examples
In Fall 2019, I taught a new course, “Simulation Techniques and Applications”. As a capstone exercise for the course, students produced tutorial web pages illustrating different simulation techniques using Gromacs, with all files needed to run the examples supplied in a tarball. The set of examples are presented in this website.
Lemkul examples
Justin Lemkul has prepared several excellent tutorial examples of Gromacs simulations, with an emphasis on biochemical applications. These include:
- A protein (lysozyme) in water, for an introduction to basic simulation files and workflow.
- A membrane protein (KALP15) in a lipid bilayer, including how to build the starting state.
- An umbrella sampling example, to obtain a potential of mean force (PMF).
- A two-phase fluid system, again showing how to build the initial configuration.
- An insertion free energy calculation, for methane in water.