School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece.
J Phys Chem B. 2010 Jun 17;114(23):7844-53. doi: 10.1021/jp908975d.
In this work we propose a methodology for improving dynamical sampling in molecular simulations via temperature acceleration. The proposed approach combines the novel methods of Voter for temperature-accelerated dynamics with the multiple histogram reweighting method of Ferrenberg and Swendsen, its dynamical extension by Nieto-Draghi et al., and with hazard plot analysis, allowing optimal sampling with small computational cost over time scales inaccessible to classical molecular dynamics simulations by utilizing the "inherent structure" idea. The time evolution of the system is viewed as a succession of transitions between "basins" in its potential energy landscape, each basin containing a local minimum of the energy (inherent structure). Applying the proposed algorithm to a glass-forming material consisting of a mixture of spherical atoms interacting via Lennard-Jones potentials, we show that it is possible to perform an exhaustive search and evaluate rate constants for basin-to-basin transitions that cover several orders of magnitude on the time scale, far beyond the abilities of any competitive dynamical study, revealing an extreme ruggedness of the potential energy landscape in the vicinity of the glass transition temperature. By analyzing the network of inherent structures, we find that there are characteristic distances and rate constants related to the dynamical entrapment of the system in a neighborhood of basins (a metabasin), whereas evidence to support a random energy model is provided. The multidimensional configurational space displays a self-similar character depicted by a fractal dimension around 2.7 (+/-0.5) for the set of sampled inherent structures. Only transitions with small Euclidean measure can be considered as localized.
在这项工作中,我们提出了一种通过温度加速来改进分子模拟动力学采样的方法。所提出的方法将 Voter 用于温度加速动力学的新方法与 Ferrenberg 和 Swendsen 的多重直方图再加权方法、Nieto-Draghi 等人的动力学扩展以及危险图分析相结合,允许通过利用“固有结构”的想法,以小的计算成本在经典分子动力学模拟无法达到的时间尺度上进行最佳采样。系统的时间演化被视为在其势能景观中的“盆地”之间连续过渡,每个盆地都包含能量的局部最小值(固有结构)。将所提出的算法应用于由通过 Lennard-Jones 势能相互作用的球形原子组成的玻璃形成材料,我们表明可以进行详尽的搜索,并评估跨越几个时间尺度的顺序的盆地到盆地的跃迁的速率常数,远远超出任何竞争动力学研究的能力,揭示了在玻璃转变温度附近势能景观的极端崎岖。通过分析固有结构网络,我们发现存在与系统在盆地(超盆地)附近的动力学捕获相关的特征距离和速率常数,而提供了支持随机能量模型的证据。多维构型空间显示出自相似特征,其在采样的固有结构集周围的分形维数约为 2.7(+/-0.5)。只有具有小欧几里得度量的跃迁才能被认为是局部的。