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The computational experiment has a vital position in modern science.Today's world is guided by computer simulation. Computer simulations have done to understand the properties of a gathering of molecules in terms of their structure and microscopic interactions. Molecular dynamics simulation (MDS) serves as a complement to conventional experiments.This book carries six chapters. First two chapters give the importance of Molecular dynamics simulation in the biological world and basic theory. The aim of the book is to familiarize you some idea about necessary of molecular dynamics simulation and its operation and applications. Third, the fourth and fifth chapter deals with GROMACS software-(operation and analysis tools). The sixth chapter gives a molecular dynamics work on an ion channel protein. The objective of this book is not to consider all parts of Gromacs simulation and analysis tools in depth, but rather to present a birds view and understanding.