Wu Yudong, Schmitt Jeffrey D, Car Roberto
Department of Chemistry and Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08540, USA.
J Chem Phys. 2004 Jul 15;121(3):1193-200. doi: 10.1063/1.1765651.
A recently proposed dynamical method [A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002)] allows us to globally sample the free energy surface. This approach uses a coarse-grained non-Markovian dynamics to bias microscopic atomic trajectories. After a sufficiently long simulation time, the global free energy surface can be reconstructed from the non-Markovian dynamics. Here we apply this scheme to study the T=0 free energy surface, i.e., the potential energy surface in coarse-grained space. We show that the accuracy of the reconstructed potential energy surface can be dramatically improved by a simple postprocessing procedure with only minor computational overhead. We illustrate this approach by conducting conformational analysis on a small organic molecule, demonstrating its superiority over traditional unbiased approaches in sampling potential energy surfaces in coarse-grained space.
最近提出的一种动力学方法[A. 莱奥和M. 帕里内洛，《美国国家科学院院刊》99, 12562 (2002)]使我们能够对自由能面进行全局采样。该方法使用粗粒化的非马尔可夫动力学来使微观原子轨迹产生偏差。经过足够长的模拟时间后，可从非马尔可夫动力学重建全局自由能面。在此，我们应用该方案来研究T = 0时的自由能面，即粗粒化空间中的势能面。我们表明，通过一个简单的后处理程序，只需少量的计算开销，就能显著提高重建势能面的精度。我们通过对一个小有机分子进行构象分析来说明这种方法，证明其在粗粒化空间中采样势能面方面优于传统的无偏差方法。
