Collective variable-based calculations in NAMD
نویسندگان
چکیده
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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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2009
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2008.12.2071