A fast mollified impulse method for biomolecular atomistic simulations

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• 作者：L. Fath^a ; ^{lukas.fath@kit.edu} ; M. Hochbruck^a ; ^{marlis.hochbruck@kit.edu} ; C.V. Singh^b ; ^{chandraveer.singh@utoronto.ca}
• 关键词：Mollified impulse method ; Highly oscillatory ; Resonances ; Corotation ; Molecular dynamics
• 刊名：Journal of Computational Physics
• 出版年：2017
• 出版时间：15 March 2017
• 年：2017
• 卷：333
• 期：Complete
• 页码：180-198
• 全文大小：2558 K
• 卷排序：333

文摘

Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.