[gmx-users] Lie method for binding free energy calculations

Sajad Ahrari sajadahrari at yahoo.com
Fri Oct 25 17:07:22 CEST 2013

Hello dears 
searching through literature, many cases of LIE method application for BFE  calculation of small molecules are on hand . but I couldn't find any report of using this method for interaction of small peptides and proteins. I wanted to know if the protocol prepared in Justin tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html) can be used in such case? and if so, should I apply any constrain on rotatable bonds of peptide along the simulation within the non-bonded state?

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