Enhanced Sampling in the Well-Tempered Ensemble
Enhanced Sampling in the Well-Tempered Ensemble
复制标题
DOI：
10.1103/physrevlett.104.190601
复制
发表时间：
2010-05-14
影响因子：
8.6
通讯作者：
Parrinello, M.
中科院分区：
文献类型：
--
作者：
Bonomi, M.;Parrinello, M.
我们介绍了脾气暴躁的合奏（WTE），这是当能量用作集体变量时，由脾气暴躁的元动力学取样的偏见集合。可以设计WTE，以使其具有与规范合奏的平均能量大致相同，但波动更大。这两种特性导致对相空间的极快探索。当WTE与平行回火合并时，获得更高的效率。公正的Boltzmann平均值是通过最近开发的重新加权方法即时计算的[M. Bonomi等人，J。Comput。化学30，1615（2009）]。我们将WTE及其平行回火变体应用于2D ISING模型，并将其在HIV蛋白酶的BAR模型上应用于G（O），在这两种代表性的情况下，通过数量级加速了收敛。
We introduce the well-tempered ensemble (WTE) which is the biased ensemble sampled by well-tempered metadynamics when the energy is used as collective variable. WTE can be designed so as to have approximately the same average energy as the canonical ensemble but much larger fluctuations. These two properties lead to an extremely fast exploration of phase space. An even greater efficiency is obtained when WTE is combined with parallel tempering. Unbiased Boltzmann averages are computed on the fly by a recently developed reweighting method [M. Bonomi et al., J. Comput. Chem. 30, 1615 (2009)]. We apply WTE and its parallel tempering variant to the 2d Ising model and to a G (o) over bar model of HIV protease, demonstrating in these two representative cases that convergence is accelerated by orders of magnitude.