Technical Note
Version 1
Preserved in Portico This version is not peer-reviewed
Practical Implementation of Molecular Dynamics Code for Beginners Using Python
Version 1
: Received: 7 December 2020 / Approved: 8 December 2020 / Online: 8 December 2020 (06:47:59 CET)
How to cite: Yesudasan, S. Practical Implementation of Molecular Dynamics Code for Beginners Using Python. Preprints 2020, 2020120179. https://doi.org/10.20944/preprints202012.0179.v1 Yesudasan, S. Practical Implementation of Molecular Dynamics Code for Beginners Using Python. Preprints 2020, 2020120179. https://doi.org/10.20944/preprints202012.0179.v1
Abstract
In this paper, we introduce a simple yet powerful and working version of the molecular dynamics code using the Python 3.9 language. The code contents are published in the link given in the appendix 1. The structure and components of the program is given in detail using flowcharts and code snippets. The program consists of major features like velocity verlet integrator, thermostats, COM removal, input and output modules, virial, pressure, and other thermodynamic quantities estimation etc. The author believes that this program will be helpful to graduate students who perform research in molecular dynamics simulations who intend to write their own code instead of the sophisticated open source packages.
Keywords
Python; Molecular Dynamics; Scientific Computing; Periodic Boundary Condition
Subject
Engineering, Automotive Engineering
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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