Development of fundamental methods for fast, accurate, and stable simulation of molecular dynamics

2015 Fiscal Year Final Research Report

• Project/Area Number: 25390156
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Computational science
• Research Institution: Osaka University
• Principal Investigator: Fukuda Ikuo 大阪大学, たんぱく質研究所, 招へい研究員(准教授) (40643185)
• Co-Investigator(Renkei-kenkyūsha): NAKAMURA Haruki 大阪大学, 蛋白質研究所, 教授 (80134485) ; MORITSUGU Kei 横浜市立大学, 生命医科学研究科, 特任准教授 (80599506)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Keywords: 分子動力学 / 相互作用計算 / 力学系 / 運動方程式 / 数値積分 / サンプリング / 数値計算

Outline of Final Research Achievements

We have developed fundamental methods for fast, accurate, and stable simulation of molecular dynamics (MD). We have considered numerical method to accurately and stably integrate the equations of motion employed in the MD. To reduce the computational cost of the MD calculation, we have developed the zero-multipole summation method, which enables both reducing drastically the cost and keeping sufficiently the accuracy to calculate the electrostatic interactions of particles in the system. The efficiency has been confirmed by applying the method to fundamental systems with estimating various quantities, including thermodynamic quantities. To solve the slow time-development of the dynamical system characteristic to the MD, we have developed a new equations of motion, the double density dynamics. We have clarified its theoretical properties, realized a stable numerical integration based on the above developed method, and validated the efficiencies by applying it to bimolecular systems.

Free Research Field

計算科学