In silico alchemy: A tutorial for alchemical FEP and TI free-energy calculations with NAMD
نویسندگان
چکیده
This tutorial explains how NAMD and related tools can be used to setup and perform alchemical freeenergy simulations, within the free-energy perturbation (FEP) and thermodynamic integration (TI) theories. The “zero-sum” transformation of ethane into ethane is used as an introductory example. FEP is then used to compute the free energy of charging a naked Lennard-Jones particle into a sodium ion. Last, the variation in solvation free energy upon mutation of a tyrosine residue into alanine is examined in the Ala–Tyr–Ala tripeptide. Prior knowledge of NAMD and standard molecular dynamics simulations is assumed. c © 2009, Centre National de la Recherche Scientifique, University of Illinois, Urbana–Champaign
منابع مشابه
In silico alchemy: A tutorial for alchemical free-energy perturbation calculations with NAMD
This tutorial explains how NAMD and related tools can be used to setup and perform alchemical freeenergy simulations within the free-energy perturbation (FEP) theory. The force-field independent, “zero-sum” transformation of ethane into ethane is used as an introductory, prototypical example. FEP is then used to compute the free energy of charging a naked Lennard-Jones particle into a sodium io...
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