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freeEaccurate - Exploring the free-energy landscapes of...

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1 Exploring the free-energy landscapes of biological systems with steered molecular dynamics Guodong Hu and L. Y. Chen* Department of Physics, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249 We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD -FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-mass coordinates of the small molecule (methane, ion, benzene, and water, respectively) is steered (pulled) at a given speed over a period time, during which the system transitions from one macroscopic state/conformation (State A) to another one (State B). The mechanical work of pulling the system is measured during the process, sampling a forward pulling path. Then the reverse pulling is conducted to sample a reverse path from B back to A. Sampling a small number of forward and reverse paths, we are able to accurately compute the free-energy profiles for all the afore-listed systems that represent various important aspects of biological physics. The numerical results are in excellent agreements with the experimental data and/or other computational studies available in the literature. 82.20.Wt, 82.37.Rs, 05.60.Cd, 05.40.Jc, 05.70.Ln *[email protected]
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