Preprint Technical Note Version 1 Preserved in Portico This version is not peer-reviewed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 (doi: 10.20944/preprints202012.0179.v1). Yesudasan, S. Practical Implementation of Molecular Dynamics Code for Beginners Using Python. Preprints 2020, 2020120179 (doi: 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.

Subject Areas

Python; Molecular Dynamics; Scientific Computing; Periodic Boundary Condition

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