Molecular Dynamics (MD) is a powerful computational strategy to analyze how complex biological molecules behave at the atomic scale. The major shortcomings of MD simulations is the high computational cost, and consequently the severe limitation on the timescales accessible by brute force MD simulations. In recent years, the realm of biological processes amenable to atomistic simulations has dramatically increased thanks to two major events: (i) the decrease in the cost of computational resources, and (ii) the development of novel algorithm to accelerate sampling and analyze atomic trajectories. Our laboratory is equipped with state-of-the-art computational facilities, and we have experience in the numerical strategies used for extending the timescales of MD simulations. By adopting these techniques we contributed to the current understanding of conduction events across membrane proteins, and to the sliding of proteins along DNA molecules. The services we offer include:

• Set-up and running of classical MD trajectories

• Free-energy calculations

• Molecular docking