Tutorials

Learning molecular dynamics simulations can appear daunting at first. “What is a cutoff?” “How do I add water to my protein?” Questions can be so numerous that the beginner has no idea where to start! That’s why a large number of tutorials have been written for helping novice (and experienced!) users alike. The largest collection of VMD and NAMD tutorials can be found at the TCBG website, but a few are also highlighted here.


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VMD Tutorial
This tutorial addresses how to use the molecular visualization program VMD to view protein structures, build systems for simulation, and analyze results.

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NAMD Tutorial
This tutorial introduces the MD-simulation package NAMD as well as details much of the setup and input.

 

 


Free Energy Tutorials

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FEP Tutorial
Alchemical free-energy perturbation allows one to change one species to another through non-physical intermediates, calculating the free energy of the process along the way.

  • Instructions: pdf
  • Required tutorial files: .tar.gz

ABF Tutorial
ABF Tutorial
Adaptive-biasing forces (ABF) is a quasi-equilibrium method for determining the potential-of-mean force (PMF) along a chosen reaction coordinate.

  • Instructions: pdf
  • Required tutorial files: .tar.gz

 

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Methods for calculating Potentials of Mean Force
Steered MD and free-energy techniques are applied to substrate translocation through the AmtB channel in this tutorial.

  • Instructions: pdf
  • Required tutorial files: .tar.gz

Tutorial
Ligand Binding Tutorial
How to calculate accurate binding constants using a staged free-energy procedure is explained in detail.

  • Instructions: pdf
  • Required tutorial files: .tar.gz