Compensating mass matrix potential for constrained molecular dynamics
Compensating mass matrix potential for constrained molecular dynamics
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DOI：
10.1006/jcph.1997.5731
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发表时间：
1997-09-15
影响因子：
4.1
通讯作者：
Jain, A
中科院分区：
文献类型：
--
作者：
Jain, A
在分子模型中使用刚性内部约束来加速分子动力学（MD）模拟。众所周知，这种约束MD模拟的统计平均值与使用常规无约束MD模拟计算的类似平均值相差一个度量张量依赖项。菲克斯曼建议用一个补偿项来增加标准势，这个补偿项依赖于度量张量来抵消这个偏置项的影响。然而，在缺乏易处理的算法来计算这种补偿张量势及其梯度的情况下，它的使用是不切实际的。本文导出了一种计算树形拓扑分子系统的补偿势及其梯度的新算法。该算法是非常简单的，是一个扩展的空间运营商为基础的O（N）算法，最近提出的约束动力学。实际上，补偿势是密切相关的，并且是根据从该O（N）算法可获得的铰接体惯性量来计算的。(C)北京：科学出版社.
Rigid internal constraints are used in molecular models to speed up molecular dynamics (MD) simulations. It is well recognized that statistical averages from such constrained MD simulations differ by a metric tensor-dependent term from similar averages computed using conventional unconstrained MD simulations. Fixman proposed augmenting the standard potential with a compensating term which depends on the metric tensor to nullify the effects of this bias term. However, in the absence of tractable algorithms to compute this compensating tensor potential and its gradient its use has been impractical. This paper derives a new algorithm for computing the compensating potential, as well as its gradient for tree topology molecular systems. The algorithm is quite straightforward and is an extension of the spatial operators based O(N) algorithm that has been recently proposed for constrained dynamics. Indeed, the compensating potential is closely related and computed from the articulated body inertia quantities available from this O(N) algorithm. (C) 1997 Academic Press.