What is Molecular Dynamics (MD) Simulation

Energy minimization is a paramount zone in the field of computational and structural biology for protein modeling. It helps in mending distorted geometries in the folded functional protein by moving its atoms to release internal constraints. It attempts to hold back to zero value for the net atomic force on every atom. But to overcome certain disadvantages in energy minimization, Simulated Annealing (SA) can be helpful. SA is a molecular dynamics technique, where temperature is gradually reduced during the simulation. It provides the best configuration of bio-molecules in shorter time. With the advancement in computational knowledge, one essential but less sensitive variant of SA: Adaptive Simulated Annealing (ASA) algorithm is beneficial, because it automatically adjusts the temperature scheme and abrupt opting of step. Therefore it benefits to prepare stable protein models and further to investigate protein-protein interactions. Thus, a residue-level study can be analyzed in details for the benefit of the entire biota.