Linking Well-Tempered Metadynamics Simulations with Experiments
Linking Well-Tempered Metadynamics Simulations with Experiments
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DOI：
10.1016/j.bpj.2010.01.033
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发表时间：
2010-05-05
影响因子：
3.4
通讯作者：
Parrinello, Michele
中科院分区：
文献类型：
--
作者：
Barducci, Alessandro;Bonomi, Massimiliano;Parrinello, Michele
Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data.
