Tutorials

Included below are a number of free energy tutorials for a variety of molecular programs. They do not necessarily all follow all of the guidelines outlined, but have generally been prepared by advanced users of the relevant codes, so should work with the. Please direct questions about the tutorials that are not hosted on Alchemistry.org to the authors of the tutorials themselves!

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 4.6.3 and later versions of GROMACS, see [[GROMACS 4.6 example: Direct ethanol solvation free energy|instructions] on how to compute ethanol solvation free energy using standard free energy calculations or Hamiltonian replica exchange, or 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.

CHARMM Tutorials

We're looking for a good CHARMM tutorial! Care to recommend one?