Free Energy Calculations with Non-Equilibrium Methods: Applications of the Jarzynski Relationship |
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| Authors: | Hui Xiong Alejandro Crespo Marcelo Marti Dario Estrin Adrian E Roitberg |
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| Institution: | (1) Quantum Theory Project and Department of Physics, University of Florida, P.O. Box 118435, Gainesville, FL 32611-8435, USA;(2) Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria – Pab II, C1428EHA Buenos Aires, Argentina |
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| Abstract: | We present an introduction to the Jarzynski relationship that makes a strong connection, for a thermodynamic transformation, between the distribution of non-equilibrium work values and the corresponding equilibrium free energy differences. The relationship is discussed in the context of sampling issues, high level parallel computing and convergence criteria. We discuss three different applications by our group: mechanical unfolding of peptides, mixed quantum/classical free energy calculations in enzymes, and ligand escape pathways |
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