Abstract:

[Objective] Molecular dynamics simulation is a powerful tool for studying the internal movement and interactions of matter at micro/meso-scales, allowing researchers to observe details that are difficult to capture experimentally. The development and optimization of the molecular dynamics software enable researchers to analyze and predict the microscopic behaviors of complex systems, driving the discovery and innovation of materials and drugs, etc. [Methods] Traditional molecular simulation software is mainly written in programming languages such as Fortran, C, and C++, and their complex code structures make it a challenge for most users to customize new features. For this reason, based on our experiences in developing the polymer molecular dynamics simulation software, we developed a molecular dynamics interpreter PyGAMD using the interpreted language Python. [Results] PyGAMD supports customized molecular dynamics functions. In addition, it includes polymer modeling tools, heterogeneous acceleration libraries, and data processing tools. With PyGAMD users can easily compose the required modules and run molecular dynamics simulations. In terms of computational efficiency, PyGAMD performs exceptionally well in most cases. The further development of PyGAMD will focus on a highly flexible multi-modular framework, as well as machine learning potentials and fine-graining functions.

Key words: molecular dynamics, coarse-grained simulation, interpreter