Morishita Tetsuya, Itoh Satoru G, Okumura Hisashi, Mikami Masuhiro
Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jun;85(6 Pt 2):066702. doi: 10.1103/PhysRevE.85.066702. Epub 2012 Jun 11.
A method for free-energy calculation based on mean-force dynamics (fictitious dynamics on a potential of mean force) is presented. The method utilizes a logarithmic form of free energy to enhance crossing barriers on a free-energy landscape, which results in efficient sampling of "rare" events. Invoking a conserved quantity in mean-force dynamics, free energy can be estimated on-the-fly without postprocessing. This means that an estimate of the free-energy profile can be locally made in contrast to the other methods based on mean-force dynamics such as metadynamics. The method is benchmarked against conventional methods and its high efficiency is demonstrated in the free-energy calculation for a glycine dipeptide molecule.
提出了一种基于平均力动力学（平均力势上的虚拟动力学）的自由能计算方法。该方法利用自由能的对数形式来增强自由能景观上的穿越势垒能力，从而实现对“稀有”事件的高效采样。通过调用平均力动力学中的一个守恒量，可以即时估计自由能，而无需进行后处理。这意味着与其他基于平均力动力学的方法（如元动力学）相比，可以在局部估计自由能分布。该方法与传统方法进行了基准测试，并在甘氨酸二肽分子的自由能计算中证明了其高效性。
