Understand NVE, NVT, and NPT ensembles in MD simulations: physical meaning, when to use each stage, and the key GROMACS mdp parameters to set.

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.

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.

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.

Explore the world of non-bonded interactions in Molecular Dynamics (MD) simulations. Learn about the different types of non-bonded interactions such as electrostatic and van der Waals interactions and their roles in MD simulations.

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.