Tuesday, March 26, 2019

What are molecular dynamics and MD simulation?

In computational chemistry, molecular dynamics (MD) simulations are when you simulate or model the motion s and behavior of individual atoms in a molecule or molecules of your choosing by applying the laws of classical mechanics to solve for parameters such as velocity, charge, position and so on. Inevitably the use of classical mechanics to describe such small particles means that one ends up relying on some parameters that should be measured (experimentally, or calculated through some ab initio method. More on this below) or known beforehand (from scientific literature). The collections of such parameters are known as forcefields. Examples for some forcefields that are used today are CHARMM and AMBER forcefields.
Molecular dynamics calculations can be less accurate than quantum mechanics calculations but are relatively a lot faster in most situations. Quantum mechanics calculations of the ab initio type don't suffer from the same crutch as MD simulations in that they calculate everything from scratch, and do not require you to provide experimental information.

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