What is a Molecular Dynamics Simulation?

in #stem2 months ago

What is Molecular Dynamics?

By means of a molecular dynamics simulation, one tries to calculate molecule or substance properties on the computer in order to make predictions for the real world. This can be, for example, the determination of the melting temperature.

How does a Molecular Dynamics Simulation Work?

The basis of molecular dynamics simulations is the calculation of forces between individual particles. Often the atoms are used as elementary particles and now one calculates the forces between the individual particles. Since atoms have electrons, there is a repulsion between atoms that are very close to each other, also called Pauli repulsion. If one really wants to calculate this exactly on a quantum mechanical level, this is very complex. Therefore, pseudopotentials are often used. These are simple mathematical functions, which are very similar to the real forces. One such function is the Lennard Jones potential.

The lennard-jones potential, Source

Now this potential and the Netwton equations can be used to determine how the atoms move relative to each other.

Image of a simple Molecular Dynamics simulation, source

Limitations of Molecular Dynamics Simulation

Molecular dynamics simulations simulate very small time spans. It is not possible to simulate processes that last a few seconds. Instead, the processes simulate only picoseconds. So for such processes one needs other procedures.


In fact, simulation helps a lot while studying the properties of a molecule. I am now using Gauss view program.
Thank you.

Thanks for sharing your thoughts =)

Hey thanks a lot for bringing this topic, computer simulations of molecules are very important also in the biomedical research world right now! It is much easier to predict how molecules can be used in new drugs for example.
thanks for the review

Yeah, I can imagine computer simulations being important in biomedical research. Interesting times =D
And thank you for curating my post =)


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