Implicit Time Integration for Multiscale Molecular Dynamics Using Transcendental Padé Approximants

详细信息    查看全文

• 作者：Andrew Abi Mansour ; Peter J. Ortoleva
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2016
• 出版时间：April 12, 2016
• 年：2016
• 卷：12
• 期：4
• 页码：1965-1971
• 全文大小：454K
• 年卷期：0
• ISSN：1549-9626

文摘

Molecular dynamics systems evolve through the interplay of collective and localized disturbances. As a practical consequence, there is a restriction on the time step imposed by the broad spectrum of time scales involved. To resolve this restriction, multiscale factorization was introduced for molecular dynamics as a method that exploits the separation of time scales by coevolving the coarse-grained and atom-resolved states via Trotter factorization. Developing a stable time-marching scheme for this coevolution, however, is challenging because the coarse-grained dynamical equations depend on the microstate; therefore, these equations cannot be expressed in closed form. The objective of this paper is to develop an implicit time integration scheme for multiscale simulation of large systems over long periods of time and with high accuracy. The scheme uses Padé approximants to account for both the stochastic and deterministic features of the coarse-grained dynamics. The method is demonstrated for a protein either undergoing a conformational change or migrating under the influence of an external force. The method shows promise in accelerating multiscale molecular dynamics without a loss of atomic precision or the need to conjecture the form of coarse-grained governing equations.