Molecular simulations provide valuable insights into the structure and function of molecular systems - enabling detailed analysis of various physical and chemical properties at the molecular or atomic level. These findings can then supplement experimental data. These simulations typically fall into two major categories: Molecular Dynamics (MD) simulations (which is what we do) and Monte Carlo (MC) methods. The former allows for time-dependent properties to be studied, while the latter is time-independent but instead allows for the equilibrium properties of the system to be studied.
In order to study molecular systems at a quantum level, one can deploy Density Functional Theory (DFT). DFT can be combined with MD in what is known as Ab Initio Molecular Dynamics.
Molecular Dynamics
Molecular Dynamics
For classical MD simulations, a starting structure is required (typically collected experimentally but can also be obtained computationally, or from a combination of the two). Atomic trajectories are generated by numerical integrating of Newton’s equations of motion. Dynamic properties of the system can then be investigated at atomic resolution.
DFT
DFT
This is a quantum-mechanical method for calculating the electronic structure of atoms and molecules. In the context of metalloenzymes, it can be used to compute the energetic and geometric properties of the metal cluster and the surroundings ligands.
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