Alchemical FEP Tutorial
A tutorial for alchemical FEP in NAMD
Jérôme Hénin and Christophe Chipot
Equipe de dynamique des assemblages membranaires
Unité Mixte de Recherche C.N.R.S./U.H.P. No 7565
Université Henri Poincaré - Nancy I
54506 Vandoeuvre-lès-Nancy, Cedex, France
March 19, 2008
This tutorial explains how NAMD and related tools can be used to setup and perform alchemical free energy simulations, within the free energy perturbation (FEP) theory. The "zero-sum" transformation of ethane into ethane is used as an introductory example. FEP is then used to compute the variation in solvation free energy upon mutation of a tyrosine residue into alanin in the Ala-Tyr-Ala tripeptide. Prior knowledge of NAMD and standard molecular dynamics simulations is assumed.
Alchemical FEP Tutorial 517k PDF
© 2006, Centre National de la Recherche Scientifique