Introduction

Molecular dynamics (MD) simulations are exceptionally important in the research field of polymers, soft matters, biomolecules, and etc. In general, all-atom or coarse-grained force fields are not easily ported between MD packages. It is quit difficult to realize a new method in a well-developed MD package by users. Thereby, we provide a MD simulation package named PYGAMD (Python GPU-Accelerated Molecular Dynamics Software) to solve these problems.

PYGAMD is a platform where users could build up their customized force fields including potential forms and parameters. This is achieved by that PYGAMD is programmed based on Numba, a Just-In-Time Python Compiler. The potential forms and methods could be conveyed from user interface to the underlying computation. More important, PYGAMD provide a high performance on GPU computation up to traditional packages programmed by CUDA and C.

This package is the version 1 of PYGAMD which includes MD engine pygamd, molecular configuration generator molgen, and data tackler dataTackle etc. The pygamd is purely written by Python language based on Python3 Numba compiler. The plugins molgen and dataTackle that are written by C++ and CUDA C, need to be compiled.