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Setting up a Molecular Dynamics simulation

Setting up a realistic simulation of a given molecular system involves different steps some of which depend on its complexity, and on the conditions we choose for our experiment. In this article, I try to explain to you which are the typical steps to perform in Molecular Dynamics (MD). However, always keep in mind that an MD simulation protocol is highly system-dependent, and each system needs to be analyzed differently.

Force Fields in Molecular Dynamics

A Force Field is a set of functional terms and parameters required to compute the potential energy equation of a molecular system. Different force fields are nowadays available. It is extremely important to know the limitations and capabilities of each one of them.

Molecular Dynamics: Bonded interactions

Bonded interactions are one of the two components building the Molecular Mechanics potential energy equation. Here you can find a detailed explanation of the various contributions to the bonding interactions and their importance in molecular modeling.

Molecular Mechanics (MM)

Molecular Mechanics is a fundamental tool in the field of molecular modeling. This technique neglects the quantum properties of a molecule and only relies on classical mechanics. As a result, complex molecular systems are approximated as simple "balls and springs" models. This allows faster calculations.