Mechanical Engineering Department, University of Tabriz, Tabriz, East Azerbaijan, 5166616471, Iran.
Research into Artifacts, Center for Engineering, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8568, Japan.
J Mol Model. 2020 Apr 20;26(5):106. doi: 10.1007/s00894-020-4349-0.
The external fields, such as the magnetic force, have made advances in many industrial and biotechnology applications during the past century, although the changes in the structure of materials under the impact of the electromagnetic fields have not entirely been clear yet. The molecular simulation technique by providing extensive data from the configuration and orientations of the atoms is becoming the effective useful tool for scientists in a wide range of research areas. This paper presents an extended velocity Verlet algorithm inside the Nanoscale Molecular Dynamics (NAMD) package that enhances the NAMD features with the capability to compute the magnetic field force. We described how this novel feature has been implemented inside the package. Moreover, the results are reported for the rotation of a charged particle, and the thermo-physical properties of water in the presence of a magnetic field confirming how this developed NAMD source code provides accurate measurements compared with other available data.
在过去的一个世纪中，外部场，如磁场，在许多工业和生物技术应用中取得了进展，尽管材料在电磁场影响下的结构变化尚不完全清楚。分子模拟技术通过提供原子构型和取向的广泛数据，正在成为广泛研究领域的科学家们的有效工具。本文提出了在 Nanoscale Molecular Dynamics (NAMD) 包中扩展的速度 Verlet 算法，该算法增强了 NAMD 的功能，使其能够计算磁场力。我们描述了如何在包中实现这个新特性。此外，还报告了在磁场存在下带电粒子的旋转和水的热物理性质的结果，证实了这个开发的 NAMD 源代码与其他可用数据相比如何提供了更准确的测量。
