Tutorials

GROMACS Tutorials

A very useful tutorial for calculating free energies in GROMACS 4.5.3 by Justin Lemkul.

For tutorial for earlier versions of Gromacs, see our original tutorial on methane insertion in water.

For tutorials for 4.6.2 versions of GROMACS, see instructions on how to run this calculation with GROMACS 4.6 using standard free energy calculations, or using using expanded ensemble simulations.

AMBER Tutorials

An AMBER tutorial for free energy calculations. This tutorial describes setting up and running free energy calculations of benzene and phenol to the T4 Lysozyme L99A model protein.

NAMD Tutorials

A tutorial for setting up free energy calculations using NAMD.

Specific problems include computing the free energy of charging a naked Lennard-Jones particle into a sodium ion, the variation in solvation free energy upon mutation of a tyrosine residue into alanine is examined in the Ala–Tyr–Ala tripeptide, and binding free energy of a potassium ion to a ionophore, 18–crown–6 ether.