Introduction to Molecular Dynamics Simulations A Practical Guide Using C/C++, FORTRAN, and Python Series in Computational Physics Series

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.

Introduction. Basic molecular dynamics. Force fields. Time integration and special numerical techniques. Vibrational analysis of molecular compounds. Static and dynamical properties of simple fluids. Parallelization. Long-range interactions and periodic boundary conditions. Complex fluids. Rigid molecules. Tight-binding force fields. ADVANCED MOLECULAR DYNAMICS SIMULATIONS. State-of-the-art molecular dynamics simulation software (Amber, Gromacs, NAMD). Molecular dynamics simulations using the NAMD package. Analysis of trajectories. Adjusting force fields to ab initio calculations