Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations

作者：Hongzhi Li, Donghong Min, Yusong Liu, Wei Yang · 发表于：The Journal of Chemical Physics · 年份：2007 · DOI：10.1063/1.2769356 · 被引用次数：42 · 研究领域：Protein Structure and Dynamics、Nanopore and Nanochannel Transport Studies、Spectroscopy and Quantum Chemical Studies

To overcome the possible pseudoergodicity problem, molecular dynamic simulation can be accelerated via the realization of an energy space random walk. To achieve this, a biased free energy function (BFEF) needs to be priori obtained. Although the quality of BFEF is essential for sampling efficiency, its generation is usually tedious and nontrivial. In this work, we present an energy space metadynamics algorithm to efficiently and robustly obtain BFEFs. Moreover, in order to deal with the associated diffusion sampling problem caused by the random walk in the total energy space, the idea in the original umbrella sampling method is generalized to be the random walk in the essential energy space, which only includes the energy terms determining the conformation of a region of interest. This essential energy space generalization allows the realization of efficient localized enhanced sampling and also offers the possibility of further sampling efficiency improvement when high frequency energy terms irrelevant to the target events are free of activation. The energy space metadynamics method and its generalization in the essential energy space for the molecular dynamics acceleration are demonstrated in the simulation of a pentanelike system, the blocked alanine dipeptide model, and the leucine model.