Applications of Molecular Dynamics Simulation

Molecular dynamics is a set of molecular simulation methods that encompass physics, mathematics, and chemistry. It mainly relies on Newtonian mechanics to simulate the motion of a molecular system and to extract samples from a system composed of different states of the molecular system, thereby calculating the configuration integral of the system. Based on the result of the integral, the thermodynamic quantities and other macroscopic properties of the system are further calculated.

Molecular Dynamics SimulationFigure 1. Molecular dynamics simulation.

Why Do We Use Molecular Dynamics?

  • Generating a thermodynamic ensemble (sampling / statistics).
  • Taking into account fluctuations/dynamics in interpretation of experimental observables.
  • Describing molecular processes free energy.
  • Help with molecular modeling.


Molecular dynamics can be used to calculate NPT, NVE, NVT and other ensembles. It is a thermodynamic calculation method based on the determinism of Newtonian mechanics. Compared with the Monte Carlo method, it has higher accuracy and validity in calculating macroscopic properties, which can be widely used in various fields such as physics, chemistry, biology, materials, and medicine. By using molecular dynamics, we can attain the following messages but not limit to:

 Applications of Molecular Dynamics Simulation

  • Potential energy function of biopolymers
  • Interactions between bonded atoms
  • Bond potential
  • Dihedral potential
  • van der Waals potential
  • Coulomb potential
  • Equilibrium properties of proteins

Examples of Applications

Molecular dynamics is used in many fields of science:

  • The first MD simulation of a simplified biological folding process was published in Nature in 1975, paving the way for the vast area of modern computational protein-folding.
  • The first MD simulation of a biological process was published in Nature in 1976, paving the way for understanding protein motion as essential in function and not just accessory.
  • MD is the standard method to treat collision cascades in the heat spike regime, i.e., the effects of energetic neutron and ion irradiation on solids and solid surfaces.

Related Services:

CD ComputaBio' molecular dynamics simulation can significantly reduce the cost of later experiments. Our molecular dynamics simulation provides accurate approximations of the behavior of real molecules and have proven to be very useful for understanding the different stages of drug development. If you are interested in our services, please contact us for more detailed information.

* For Research Use Only.