Free Energy Perturbation

From: Javad Noroozi (noroozi_javad_at_ymail.com)
Date: Tue Feb 25 2014 - 00:36:30 CST

Dear NAMD users, I know that NAMD require a dual topology for initial and final states, in order to perform FEP calculation, if all solute atoms disappear(solute turn to an ideal gas particle) when moving from lambda 1 to lambda 0 , should the solute topology be used as the dual topology? I also need derivative of Hamiltonian vs coupling parameter, how can i get this from NAMD? Javad Noroozi Chemical Engineering Department Sharif University ofTechnology Email: jnoroozi_at_che.sharif.ir

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