We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled...
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides ... A Barducci,G Bussi,M Parrinello - 《Physical Review Letters...
3、建议读一下metadynamics的原文，理解各个参数的含义 4、reweighting是把一个反应坐标空间内的结果转换到...
well-tempered 听听怎么读 英['welt'empəd] 美['welt'empəd] 是什么意思 adj. 脾气好的; 学习怎么用 权威例句 Well-tempered metadynamics: a smoothly converging and tunable free-energy method. The well-tempered neutralino A well-tempered density functional theory of electrons in molecules....
drug derivatives for KRAS-G12D: free-energy surfaces in aqueous solution by well-tempered metadynamics simulations Home All Journals Physical Sciences Molecular Physics List of Issues Volume 122, Issue 21-22 In silico drug derivatives for KRAS-G12D ... ...
(2009) Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. J. Comput. Chem. 30, 1615-1621Bonomi, M.; Barducci, A.; Parrinello, M. Reconstructing the Equilibrium Boltzmann Distribution from Well-Tempered Metadynamics. J. Comput. Chem. 2009, 30 (11), 1615- 1621...
The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations exp...
TMPRSS2 inhibitors can also fight against respiratory viruses that employ them for cell entry. Our study combining virtual screening, all-atom molecular dynamics, and well-tempered metadynamics simulation identifies vicenin-2, neohesperidin, naringin, and rhoifolin as promising TMPRSS2 antagonists. The...
well‐tempered metadynamicsWe explored the stability of the dengue virus envelope (E) protein dimer since it is widely assumed that the E protein dimer is stabilized by drug ligands or antibodies in an acidic environment, neutralizing the virus's ability to fuse with human cells. During this ...
(2009) Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. J. Comput. Chem. 30, 1615-1621Bonomi, M.; Barducci, A.; Parrinello, M. Reconstructing the equilibrium Boltzmann distri- bution from well-tempered metadynamics. J. Comput. Chem. 2009, 30, 1615-1621....