华东师范大学学报（自然科学版） >

2019 , Vol. 2019 >Issue 1: 83 - 92

DOI: https://doi.org/10.3969/j.issn.1000-5641.2019.01.010

物理学与电子学

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
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  • 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
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.

收稿日期: 2017-09-20

  网络出版日期: 2019-01-24

基金资助

国家自然科学基金（21773066）

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

  • LI Peng-fei ,
  • WANG Mei-ting ,
  • MEI Ye
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  • State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China

Received date: 2017-09-20

  Online published: 2019-01-24

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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

本文引用格式

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 . DOI: 10.3969/j.issn.1000-5641.2019.01.010

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

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