Maragliano Luca, Vanden-Eijnden Eric, Roux Benoît
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA, and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.
J Chem Theory Comput. 2009 Aug 31;5(10):2589-2594. doi: 10.1021/ct900279z.
Milestoning is a method aimed at reconstructing the statistical properties of the long-time dynamics of a system by exploiting the crossing statistics of a set of hypersurfaces, called the "milestones", placed along the reaction coordinate [Faradjian and Elber, J. Chem. Phys.2004, 120, 10880]. Recently, Vanden-Eijnden and Venturoli [J. Chem. Phys.2009, 130, 194101] showed that when a complete Voronoi tessellation of the configurational space is available, milestoning can be reformulated to utilise the statistics from a series of independent simulations, each confined within a single cell via strict reflections at the boundaries. As a byproduct, this "Voronoi tessellated milestoning" method also permits to compute the free energy of the tessellation. Here, the method is extended to support the usage of differentiable restraining potentials to confine the trajectories within each cell.
里程碑法是一种旨在通过利用沿着反应坐标放置的一组称为“里程碑”的超曲面的穿越统计来重构系统长时间动力学统计特性的方法[法拉吉安和埃尔伯，《化学物理杂志》2004年，120卷，10880页]。最近，范登艾恩德和文图罗利[《化学物理杂志》2009年，130卷，194101页]表明，当构型空间的完整沃罗诺伊镶嵌可用时，里程碑法可以重新表述为利用一系列独立模拟的统计数据，每个模拟通过在边界处的严格反射限制在单个单元格内。作为副产品，这种“沃罗诺伊镶嵌里程碑法”还允许计算镶嵌的自由能。在此，该方法得到扩展，以支持使用可微约束势将轨迹限制在每个单元格内。
