Laboratory of Protein Informatics, Research Center for Structural Biology, Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
J Chem Phys. 2011 Jan 14;134(2):024109. doi: 10.1063/1.3517105.
We propose a novel application of the Wang-Landau method (WLM) for multicanonical molecular dynamics (McMD) simulations. Originally, WLM was developed for Monte Carlo (MC) simulations. Fundamentally, WLM remarkably reduces simulation efforts because it estimates the optimal multicanonical energy function automatically. When WLM is applied to McMD, not only the multicanonical energy but also energy gradient must be estimated adequately. However, because of the rugged multicanonical energy function at the early simulation stage, applications of WLM for MD simulations are difficult and require a smoothing procedure: simulation efforts such as cubic-spline extrapolation and gathering multiple preruns are utilized for smoothing. We propose a simple and effective smoothing method that requires only one additional equation and two time-dependent parameters. As a result, our method produced the correct multicanonical energy function and succeeded in the flat sampling of a small biomolecule with reduced simulation effort.
我们提出了一种将 Wang-Landau 方法 (WLM) 应用于多正则分子动力学 (McMD) 模拟的新方法。最初，WLM 是为蒙特卡罗 (MC) 模拟开发的。从根本上讲，WLM 通过自动估计最优的多正则能量函数，显著减少了模拟工作量。当 WLM 应用于 McMD 时，不仅需要充分估计多正则能量，还需要估计能量梯度。然而，由于早期模拟阶段多正则能量函数的崎岖不平，WLM 在 MD 模拟中的应用具有一定难度，需要进行平滑处理：利用三次样条外推和收集多个预运行等模拟工作量来进行平滑处理。我们提出了一种简单有效的平滑方法，该方法仅需要增加一个额外的方程和两个时间相关的参数。因此，我们的方法产生了正确的多正则能量函数，并成功地在减少模拟工作量的情况下对小分子进行了平坦采样。
