The following tutorials cover multiple free-energy and potential-of-mean-force calculation methods using NAMD.

  • Protein:ligand Standard Binding Free Energies: A Tutorial for Alchemical and Geometrical Transformations (pdf, 2.8M) (required tutorial files [.tar.gz, 11.3M])
    This tutorial sets out to demonstrate that the standard binding free energy of a protein:ligand complex can be determined accurately by means of restrained computer simulations. In the tutorial, calculation of the contribution due to restraints follows two distinct routes, an alchemical one and a geometrical one. The methodology is illustrated by the association of a small, proline-rich peptide to a tyrosine kinase.

  • A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD (pdf, 651k) (required tutorial files [.tar.gz, 2.1M], [.zip, 2.1M], individual files)
    For users seeking to learn about a specific use of NAMD. Discusses setting up the system and calculations needed for free energy calculations of alchemical transformations within NAMD.

  • A Tutorial on Adaptive Biasing Force Calculations in NAMD (pdf, 1.1M) (required tutorial files [.tar.gz, 38.5M], [.zip, 38.5M], individual files)
    For users seeking to learn about a specific use of NAMD. Discusses setting up the system and calculations needed for adaptive biasing force calculations of conformational transitions within NAMD.

  • Stretching Deca-Alanine (html) (pdf, 1.4M) (required tutorial files [.tar.gz, 5.3M], [.zip, 5.3M], individual files)
    Provides participants with an introduction of interactive molecular dynamics and steered molecular dynamics simulations, and to the calculation of potential mean force from trajectories obtained with steered molecular dynamics simulations. Requires VMD and NAMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.

  • Forcing Substrates Through Channels (pdf, 945k) (required tutorial files [.tar.gz, 54.2M], [.zip, 54.2M], individual files)
    In this tutorial, applications of steered molecular dynamics and adaptive biasing forces to the ammonium transporter AmtB are explored. Steered molecular dynamics will be used first to gain an approximate knowledge of the permeation pathway and the barriers along it. Then, the potential mean of force for ammonia in the central region of the channel is calculated using adaptive biasing forces. The appropriate choice of parameters and potential difficulties will also be discussed. Requires VMD, NAMD, and a plotting program.

Tutorials and Resources

References: Emacs reference card (pdf) • Vi reference card (pdf) • Mac OSX Primer (html) (pdf) • Unix Primer (html) (pdf)
Contacts: Suggest an idea for a tutorialTutorial-l mailing listarchive of tutorial-l mailings
Case studies: water DNA lipid bilayers BPTIubiquitin myoglobinaquaporin ion channels titin lh2

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