The term “Molecular Dynamics” represents a group of molecular simulation techniques that incorporate Physics, Mathematics, and Chemistry. It utilizes Newtonian mechanics to mimic the movement of a molecular system and to retrieve samples from a system made up of distinct states of the molecular system, culminating in the determination of the system’s integral configuration. The thermodynamic quantities and other macroscopic properties of the system are then determined using the integrated result.
Why Molecular Dynamics?
- Building a thermodynamic ensemble (sampling and statistics).
- Considering fluctuations and dynamics when interpreting experimental variables.
- Defining the free energy of molecular mechanisms.
- Assistance in molecular modeling
Molecular dynamics is used in many fields of science:
- In 1975, Nature published the first MD simulation of a truncated biological folding process, thereby establishing the groundwork for the vast discipline of current computational protein folding.
- In 1976, Nature presented the first MD simulation of a biological process, creating opportunities for understanding protein motion as a function rather than an accessory.
- MD is the conventional method for dealing with heat spike collision cascades, i.e., the effects of energetic neutron and ion irradiation on solids and solid surfaces.