Introduction to Molecular Dynamics Simulations

This book provides an in-depth introduction to molecular dynamics (MD) simulation, the basis for computational study of complex atomic and molecular systems. The author clarifies the role of different variables and sequences throughout, avoids excessive mathematical detail, emphasizes graphical representations, and highlights illustrative applications in materials science, biology, and biochemistry. The text also presents tips for speeding up calculations and parallelization techniques based on OpenMP. The final section offers hands-on training to open-source MD codes (NAMD) and associated post-processing.