Parallelization of Molecular Dynamics Simulations Using Verlet Algorithm and OpenMP

Molecular Dynamics (MD) simulations provide qualitative insights into the dynamics of liquids, solids, and liquid–solid interfaces under varying temperature and pressure conditions. Accurate force calculations for ion cores are crucial for the success of classical MD simulations. This research explores the application of MD simulations to study large-scale systems and understand atom structure and interactions. MD simulations can successfully examine protein dynamics, such as folding and unfolding, contributing to a better understanding of their behavior. Integrating MD simulations with experimental data enables a holistic examination of atomic-level properties and their impact on cellular behavior. Additionally, MD simulations offer valuable insights into protein–ligand interactions and facilitate drug development. This study introduces an innovative optimization technique that uses the Verlet algorithm with OpenMP to parallelize MD simulations, resulting in significant computing time reductions for force and energy evaluations. This optimization methodology shows promise in various domains, including protein–ligand interactions and complex system investigations. The results show that, when compared to the serialization simulation, the proposed approach can deal with computational load balancing challenges better and more effectively, while also reducing computing time.