平衡态与非平衡态分子溶剂化自由能的计算效率比较

doi:10.3969/j.issn.1000-5641.2019.01.010

华东师范大学学报(自然科学版) ›› 2019, Vol. 2019 ›› Issue (1): 83-92.doi: 10.3969/j.issn.1000-5641.2019.01.010

平衡态与非平衡态分子溶剂化自由能的计算效率比较

李鹏飞, 王美婷, 梅晔

华东师范大学精密光谱科学与技术国家重点实验室, 上海 200062

收稿日期:2017-09-20 出版日期:2019-01-25 发布日期:2019-01-24
通讯作者: 梅晔,男,研究员,博士生导师,研究方向为计算生物物理.E-mail:ymei@phy.ecnu.edu.cn E-mail:ymei@phy.ecnu.edu.cn
作者简介:李鹏飞,男,博士研究生,研究方向为计算生物物理.E-mail:alan.pengfeili@stu.ecnu.edu.cn.
基金资助:
国家自然科学基金（21773066）

Comparison of the efficiency of equilibrium and nonequilibrium molecular dynamic simulations of molecular solvation free energies

LI Peng-fei, WANG Mei-ting, MEI Ye

State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China

Received:2017-09-20 Online:2019-01-25 Published:2019-01-24

摘要/Abstract

摘要： 着眼于13个中性氨基酸侧链类似物在水中的溶剂化自由能的计算，来比较两种计算自由能的平衡态动力学模拟和非平衡态动力学模拟方法在高性能计算机上的表现.研究发现，利用非平衡态动力学模拟来计算自由能除了在准确度上和平衡态动力学模拟的计算一致之外，在计算效率和实际所需时间上，非平衡方法计算效率更高，实际所需时间更少.

关键词: 溶剂化自由能, 氨基酸侧链类似物, 平衡态动力学模拟, 非平衡态动力学模拟

Abstract: In this study, we used calculations to determine the solvation free energies of 13 side chain analogs of neutral amino acids in water to compare the performance of equilibrium and nonequilibrium molecular dynamic simulations on high-performance computers. We found that nonequilibrium molecular dynamic simulations have the same accuracy as equilibrium molecular dynamic simulations in calculations for solvation free energies. From the perspective of efficiency and computational cost, the nonequilibrium method is more efficient and requires less computational time.

Key words: solvation free energies, side chain analogs of amino acids, equilibrium molecular dynamic simulations, nonequilibrium molecular dynamic simulations

中图分类号:

O469

李鹏飞, 王美婷, 梅晔. 平衡态与非平衡态分子溶剂化自由能的计算效率比较[J]. 华东师范大学学报(自然科学版), 2019, 2019(1): 83-92.

LI Peng-fei, WANG Mei-ting, MEI Ye. Comparison of the efficiency of equilibrium and nonequilibrium molecular dynamic simulations of molecular solvation free energies[J]. Journal of East China Normal University(Natural Sc, 2019, 2019(1): 83-92.

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平衡态与非平衡态分子溶剂化自由能的计算效率比较

Comparison of the efficiency of equilibrium and nonequilibrium molecular dynamic simulations of molecular solvation free energies

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