EXTENDED ABSTRACT: It is a daunting challenge to simulate polymers by molecular dynamics (MD) simulations due to the large size and long relaxation time of polymer chains. Combining coarse-grained models and GPU-accelerated computation, we develop a software for the large-scale MD simulations of polymers. The name of software is PYGAMD (Python GPU-Accelerated Molecular Dynamics Software, http://pygamd.com/, Fig. 1). It integrates modeling, dynamic simulation engine, property analysis modules with 9 innovative simulation methods. Taking dynamic bond model as an example, we show how to employ MD simulation method to reveal the mechanism of enhancing the mechanical properties of polymers by hydrogen or coordinate bond interactions.
Keywords：polymer simulation; molecular dynamics; PYGAMD
You-Liang Zhu is a Research Fellow and Doctoral Supervisor at the College of Chemistry, Jilin University. In 2013, he received his PhD under the supervision of Professor Zhong-Yuan Lu from Jilin University. He then joined in the Changchun Institute of Applied Chemistry, Chinese Academy of Sciences and moved back to Jilin University in 2021. He is committed to developing molecular dynamics simulation methods and software for polymers. He proposed a "dynamic bond" model to describe dynamic covalent bonds, hydrogen bonds, coordination bonds, etc. at coarse-grained level, and developed GALAMOST (J. Compute. Chem. 34, 2197, 2013) and PYGAMD (http://pygamd.com/) software. More than 200 papers of the software application have been published in internationally famous journals such as Science. As first or corresponding author, he has published over 50 papers in journals including Nat. Electron., Nat. Commun., Adv. Mater., ACS Nano and Nano Lett. and 6 software copyrights. He has hosted the Youth Program and General Program (2 projects) from the National Natural Science Foundation, as well as multiple projects from enterprises or universities.