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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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