The book "Molecular Dynamics Simulation: GROMACS Software and Its Application" offers a comprehensive introduction to molecular dynamics and its application in modern science. It highlights the importance of computer simulations for analyzing the properties of molecular assemblies and their microscopic interactions. In six chapters, it first presents the relevance of molecular dynamics in biological contexts as well as the fundamental theory. The subsequent chapters focus on the GROMACS software, including its operation and analysis tools. The book concludes with a case study on the molecular dynamics of an ion channel protein. The aim is to provide a fundamental understanding of how molecular dynamics works and its applications, without addressing all aspects of GROMACS simulation in detail.