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Gewählte Publikation:

de Ruiter, A; Petrov, D; Oostenbrink, C.
(2021): Optimization of Alchemical Pathways Using Extended Thermodynamic Integration
J CHEM THEORY COMPUT. 2021; 17(1): 56-65. FullText FullText_BOKU

Thermodynamic integration (TI) is a commonly used method to determine free-energy differences. One of its disadvantages is that many intermediate lambda-states need to be sampled in order to be able to integrate accurately over . Here, we use the recently introduced extended TI to study alternative parameterizations of H(lambda) and its influence on the smoothness of the curves as well as the efficiency of the simulations. We find that the extended TI approach can be used to select curves of low curvature. An optimal parameterization is suggested for the calculation of hydration free energies. For calculations of relative binding free energies, we show that optimized parameterizations of the Hamiltonian in the unbound state also effectively lower the curvature in the bound state of the ligand.
Autor*innen der BOKU Wien:
De Ruiter Anita
Oostenbrink Chris
Petrov Drazen
BOKU Gendermonitor:

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