Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap
Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap
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DOI：
10.1063/1.3660208
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发表时间：
2011-12-14
影响因子：
4.4
通讯作者：
Kralova, Blanka
中科院分区：
文献类型：
--
作者：
Spiwok, Vojtech;Kralova, Blanka
分子中的原子运动不是线性的。这表明非线性降维方法在分析集体原子运动时可以优于线性降维方法。此外，非线性集体运动可以用作有偏模拟技术的潜在有效指南。在这里，我们提出了一种模拟，其偏置势作用于由非线性降维方法确定的集体运动方向。正如 Brown 及其同事所描述的那样，通过 Isomap 方法分析了反式、反式 1,2,4-三氟环辛烷的临时生成构象，将这些 72 维坐标映射到三维空间 [J.化学。物理。 129, 064118 (2008)]。采用三维嵌入作为集体变量的元动力学被应用于探索所研究系统的所有相关构象并计算其构象自由能表面。该方法对所有相关构象（船、船椅和冠）以及无偏模拟无法访问的相应过渡结构进行了采样。该方案允许在有偏差的模拟中使用系统的任何参数作为集体变量。此外，我们用于将样本外构象从 72D 空间映射到 3D 空间的方案可以用作降维的通用映射，超出分子建模的范围。 (C) 2011 年美国物理研究所。 [doi:10.1063/1.3660208]
Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans, trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transition structures inaccessible by an unbiased simulation. This scheme allows to use essentially any parameter of the system as a collective variable in biased simulations. Moreover, the scheme we used for mapping out-of-sample conformations from the 72D to 3D space can be used as a general purpose mapping for dimensionality reduction, beyond the context of molecular modeling. (C) 2011 American Institute of Physics. [doi:10.1063/1.3660208]