Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.

Journal of Chemical Theory and Computation
Yu-Ming M HuangYinglong Miao

Abstract

Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recove...Continue Reading

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Citations

Oct 30, 2018·Expert Opinion on Drug Discovery·Apurba Bhattarai, Yinglong Miao
Sep 5, 2019·International Journal of Molecular Sciences·Chetna TyagiFerenc Ötvös
Aug 24, 2018·The Journal of Chemical Physics·Brian K RadakBenoît Roux
Aug 6, 2020·The Journal of Chemical Physics·James C PhillipsEmad Tajkhorshid
May 18, 2021·The Journal of Physical Chemistry Letters·Apurba BhattaraiYinglong Miao
Nov 5, 2019·Accounts of Chemical Research·Haohao FuChristophe Chipot
Jun 17, 2020·Journal of Chemical Information and Modeling·Zoe CourniaWoody Sherman
Jan 28, 2020·Journal of Chemical Information and Modeling·Kira A ArmacostZoe Cournia
Sep 17, 2020·Journal of Chemical Information and Modeling·Tai-Sung LeeDarrin M York
Dec 23, 2021·Physical Chemistry Chemical Physics : PCCP·Anna S KamenikSereina Riniker

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