Chemical Physics Letters, Vol.662, 327-332, 2016
Flexible binding simulation by a novel and improved version of virtual-system coupled adaptive umbrella sampling
Virtual-system coupled adaptive umbrella sampling (VAUS) enhances sampling along a reaction coordinate by using a virtual degree of freedom. However, VAUS and regular adaptive umbrella sampling (AUS) methods are yet computationally expensive. To decrease the computational burden further, improvements of VAUS for all-atom explicit solvent simulation are presented here. The improvements include probability distribution calculation by a Markov approximation; parameterization of biasing forces by iterative polynomial fitting; and force scaling. These when applied to study Ala-pentapeptide dimerization in explicit solvent showed advantage over regular AUS. By using improved VAUS larger biological systems are amenable. (C) 2016 Elsevier B.V. All rights reserved.
Keywords:Adaptive umbrella sampling (AUS);Virtual-system coupled AUS;Markov approximated probability distribution;Force-bias parameterization;Binding free-energy landscape