Citation: Shule Liu. Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments[J]. University Chemistry, ;2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029 shu

Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments

Shule Liu ^,

School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China

Corresponding author: Shule Liu, liushle@mail.sysu.edu.cn
Received Date: 10 October 2023
Revised Date: 18 December 2023

This article presents a series of molecular dynamics experiments employing the SPC/E water model, which have been incorporated into the author’s undergraduate computational materials science course. The SPC/E water model is renowned for its simplicity, efficiency, and accessibility, particularly for undergraduate students. These experiments encompass the validation of molecular dynamics algorithms, as well as the computation of radial distribution functions, specific heat capacity, and transport properties. These experimental components establish a direct link with the theoretical contents covered in the course, such as the fundamental principles of molecular dynamics, and the computation of material structure, thermodynamic properties, and dynamical properties. This design facilitates students’ comprehension of the fundamental principles of molecular dynamics. Furthermore, these experiments utilize the same model system and open-source software LAMMPS for all simulations, thereby minimizing computational resource requirements. Consequently, the teaching of molecular dynamics experiments in the context of computational chemistry and computational materials science courses is both uncomplicated and efficient.
- Molecular dynamics,
- Water,
- Computational chemistry,
- Computational materials science,
- Teaching Practice
1. [1]
2. [2]
3. [3]
4. [4]
5. [5]
6. [6]
  Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem.1987, 91 (24), 6269.
7. [7]
  Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys.1977, 23 (3), 327.
8. [8]
  Plimpton, S. J. Comput. Phys.1995, 117 (1), 1.
9. [9]
10. [10]
  Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, UK, 2017.
11. [11]
  Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys.1982, 76 (1), 637.
12. [12]
  Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graph.1996, 14 (1), 33.
13. [13]
  Rodgers, J. M.; Weeks, J. D. J. Chem. Phys.2009, 131 (24), 244108.
14. [14]
15. [15]
16. [16]
1. [1]
  Zhenming Xu , Mingbo Zheng , Zhenhui Liu , Duo Chen , Qingsheng Liu . Experimental Design of Project-Driven Teaching in Computational Materials Science: First-Principles Calculations of the LiFePO₄ Cathode Material for Lithium-Ion Batteries. University Chemistry, 2024, 39(4): 140-148. doi: 10.3866/PKU.DXHX202307022
2. [2]
  Xianfei Chen , Wentao Zhang , Haiying Du . Experimental Design of Computational Materials Science Based on Scientific Research Cases. University Chemistry, 2025, 40(3): 52-61. doi: 10.3866/PKU.DXHX202403112
3. [3]
  Yiying Yang , Dongju Zhang . Elucidating the Concepts of Thermodynamic Control and Kinetic Control in Chemical Reactions through Theoretical Chemistry Calculations: A Computational Chemistry Experiment on the Diels-Alder Reaction. University Chemistry, 2024, 39(3): 327-335. doi: 10.3866/PKU.DXHX202309074
4. [4]
  Renqing Lü , Shutao Wang , Fang Wang , Guoping Shen . Computational Chemistry Aided Organic Chemistry Teaching: A Case of Comparison of Basicity and Stability of Diazine Isomers. University Chemistry, 2025, 40(3): 76-82. doi: 10.12461/PKU.DXHX202404119
5. [5]
  Xiaohui Li , Ze Zhang , Jingyi Cui , Juanjuan Yin . Advanced Exploration and Practice of Teaching in the Experimental Course of Chemical Engineering Thermodynamics under the “High Order, Innovative, and Challenging” Framework. University Chemistry, 2024, 39(7): 368-376. doi: 10.3866/PKU.DXHX202311027
6. [6]
  Wanmei Li , Yingying Weng , Shouchun Yin . Teaching Reform and Practice in Professional English Courses for Graduate Students Majoring in Materials and Chemical Engineering. University Chemistry, 2024, 39(6): 63-71. doi: 10.3866/PKU.DXHX202310135
7. [7]
  Jing Li , Lin Tian , Zhao Li , Yan Chen , Zongfei Yang , Huanhuan Shi . Exploration and Practice of the “134” Ideological and Political Teaching Model in the Introduction to Applied Chemistry. University Chemistry, 2024, 39(8): 7-15. doi: 10.3866/PKU.DXHX202311047
8. [8]
  Yanan Jiang , Yuchen Ma . Brief Discussion on the Electronic Exchange Interaction in Quantum Chemistry Computations. University Chemistry, 2025, 40(3): 10-15. doi: 10.12461/PKU.DXHX202402058
9. [9]
  Hongting Yan , Aili Feng , Rongxiu Zhu , Lei Liu , Dongju Zhang . Reexamination of the Iodine-Catalyzed Chlorination Reaction of Chlorobenzene Using Computational Chemistry Methods. University Chemistry, 2025, 40(3): 16-22. doi: 10.12461/PKU.DXHX202403010
10. [10]
  Yi Li , Zhaoxiang Cao , Peng Liu , Xia Wu , Dongju Zhang . Revealing the Coloration and Color Change Mechanisms of the Eriochrome Black T Indicator through Computational Chemistry and UV-Visible Absorption Spectroscopy. University Chemistry, 2025, 40(3): 132-139. doi: 10.12461/PKU.DXHX202405154
11. [11]
  Qian Huang , Zhaowei Li , Jianing Zhao , Ao Yu . Quantum Chemical Calculations Reveal the Details Below the Experimental Phenomenon. University Chemistry, 2024, 39(3): 395-400. doi: 10.3866/PKU.DXHX202309018
12. [12]
  Hongxia Yan , Weixu Feng , Junyan Yao , Wei Tian , Rui Wang . Illuminating the Teaching of Science and Engineering Graduate Courses with “Curriculum Ideology and Politics”. University Chemistry, 2024, 39(6): 122-127. doi: 10.3866/PKU.DXHX202310059
13. [13]
  Congying Lu , Fei Zhong , Zhenyu Yuan , Shuaibing Li , Jiayao Li , Jiewen Liu , Xianyang Hu , Liqun Sun , Rui Li , Meijuan Hu . Experimental Improvement of Surfactant Interface Chemistry: An Integrated Design for the Fusion of Experiment and Simulation. University Chemistry, 2024, 39(3): 283-293. doi: 10.3866/PKU.DXHX202308097
14. [14]
  Xiaochen Zhang , Fei Yu , Jie Ma . 多角度数理模拟在电容去离子中的前沿应用. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-. doi: 10.3866/PKU.WHXB202311026
15. [15]
  Yanhui Zhong , Ran Wang , Zian Lin . Analysis of Halogenated Quinone Compounds in Environmental Water by Dispersive Solid-Phase Extraction with Liquid Chromatography-Triple Quadrupole Mass Spectrometry. University Chemistry, 2024, 39(11): 296-303. doi: 10.12461/PKU.DXHX202402017
16. [16]
  Yaping Li , Sai An , Aiqing Cao , Shilong Li , Ming Lei . The Application of Molecular Simulation Software in Structural Chemistry Education: First-Principles Calculation of NiFe Layered Double Hydroxide. University Chemistry, 2025, 40(3): 160-170. doi: 10.12461/PKU.DXHX202405185
17. [17]
  Xuyang Wang , Jiapei Zhang , Lirui Zhao , Xiaowen Xu , Guizheng Zou , Bin Zhang . Theoretical Study on the Structure and Stability of Copper-Ammonia Coordination Ions. University Chemistry, 2024, 39(3): 384-389. doi: 10.3866/PKU.DXHX202309065
18. [18]
  Baitong Wei , Jinxin Guo , Xigong Liu , Rongxiu Zhu , Lei Liu . Theoretical Study on the Structure, Stability of Hydrocarbon Free Radicals and Selectivity of Alkane Chlorination Reaction. University Chemistry, 2025, 40(3): 402-407. doi: 10.12461/PKU.DXHX202406003
19. [19]
  Zhenming Xu , Yibo Wang , Zhenhui Liu , Duo Chen , Mingbo Zheng , Laifa Shen . Experimental Design of Computational Materials Science and Computational Chemistry Courses Based on the Bohrium Scientific Computing Cloud Platform. University Chemistry, 2025, 40(3): 36-41. doi: 10.12461/PKU.DXHX202403096
20. [20]
  Dexin Tan , Limin Liang , Baoyi Lv , Huiwen Guan , Haicheng Chen , Yanli Wang . Exploring Reverse Teaching Practices in Physical Chemistry Experiment Courses: A Case Study on Chemical Reaction Kinetics. University Chemistry, 2024, 39(11): 79-86. doi: 10.12461/PKU.DXHX202403048

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(184)
HTML views(32)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142