Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.
A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.
Li
Hongzhi
H
School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA.
Fajer
Mikolai
M
Yang
Wei
W
D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D019563:Mechanics; D008956:Models, Chemical; D008958:Models, Molecular; D011789:Quantum Theory; D013816:Thermodynamics
D001704:Biopolymers