Molecular Modelling and Dynamics

Molecular modelling is a combined term for theoretical and computational techniques used to simulate or model the behaviour of molecules. 
The structure, dynamics, and thermodynamics of inorganic, biological, and polymeric systems are now frequently investigated using molecular modelling methods. Protein folding, enzyme catalysis, protein stability, conformational changes related with biomolecular function, and molecular recognition of proteins, DNA, and membrane complexes are some of the forms of biological activity that have been examined using molecular modelling.

Popular software for molecular modelling:

•    Agile Molecule
•    BALLView
•    Cerius2
•    GAUSSIAN
•    Ghemical
•    GROMOS
•    InsightII
•    MarvinSpace
•    MMTK
•    MOE
•    Molsoft ICM
•    NOCH
•    Oscail X
•    PyMOL
•    Sirius
•    SPARTAN
•    Sybyl
•    VMD

There are four primary types of molecular models: skeletal or line; stick; ball-and-stick; and space-filled or CPK.

Molecular dynamics (MD) is a computer simulation technique for investigating the atomic and molecular motions. Atoms and molecules are allowed to interact over a predetermined amount of time, revealing the system's dynamic "evolution." In the most prevalent model, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are typically calculated using interatomic potentials or molecular mechanical force fields.

Because molecular systems often consist of a large number of particles, it is impractical to analyse their properties; Molecular Dynamics simulation circumvents this issue by using numerical approaches.