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Spatial averaging for small molecule diffusion in condensed phase environments

机译:凝聚相环境中小分子扩散的空间平均

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Spatial averaging is a new approach for sampling rare-event problems. The approach modifies the importance function which improves the sampling efficiency while keeping a defined relation to the original statistical distribution. In this work, spatial averaging is applied to multidimensional systems for typical problems arising in physical chemistry. They include (I) a CO molecule diffusing on an amorphous ice surface, (II) a hydrogen molecule probing favorable positions in amorphous ice, and (III) CO migration in myoglobin. The systems encompass a wide range of energy barriers and for all of them spatial averaging is found to outperform conventional Metropolis Monte Carlo. It is also found that optimal simulation parameters are surprisingly similar for the different systems studied, in particular, the radius of the point cloud over which the potential energy function is averaged. For H_2 diffusing in amorphous ice it is found that facile migration is possible which is in agreement with previous suggestions from experiment. The free energy barriers involved are typically lower than 1 kcal/mol. Spatial averaging simulations for CO in myoglobin are able to locate all currently characterized metastable states. Overall, it is found that spatial averaging considerably improves the sampling of configurational space.
机译:空间平均是一种采样稀有事件问题的新方法。该方法修改了重要性函数,从而在保持与原始统计分布的定义关系的同时提高了采样效率。在这项工作中,将空间平均应用于物理化学中出现的典型问题的多维系统。它们包括(I)在无定形冰表面扩散的CO分子,(II)在无定形冰中探测有利位置的氢分子,以及(III)在肌红蛋白中的CO迁移。该系统涵盖了各种各样的能量屏障,并且对于所有这些能量屏障,其空间平均性能均优于传统的蒙特卡洛大都市。还发现,对于所研究的不同系统,最佳仿真参数令人惊讶地相似,特别是对势能函数进行平均的点云半径。对于H_2在非晶冰中的扩散,发现容易迁移是可能的,这与实验先前的建议是一致的。所涉及的自由能垒通常低于1 kcal / mol。肌红蛋白中CO的空间平均模拟能够找到所有当前表征的亚稳态。总的来说,发现空间平均大大改善了配置空间的采样。

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