Molecular Modelling and Dynamics

Molecular modelling involves the hypothetical and computational procedures which are used to mimic the behaviour of macromolecules. Molecular modelling techniques are used in various fields some of which are drug design, computational chemistry, materials science and computational biology. These methods are used for studying and understanding the properties of the molecules. One of the major applications of molecular modelling is molecular simulation. This is the technique which uses powerful computers to simulate the interactions between atoms and to understand the properties of materials. Such simulations involve methods that range from very detailed quantum mechanical calculations on atoms to coarse-grained classical dynamics of large groups of molecules on a timescale of milliseconds or longer.

Molecular dynamics (MD) deals with the study of physical movements of the atoms and molecules using computer simulation method, so it is referred to as one of the type of N-body simulation. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic evolution of the system. The trajectories of atoms and molecules are commonly determined by solving them numerically using Newton’s equations of motion for a group of collaborating particles. The forces between the particles and their potential energies are calculated using inter-atomic potentials or molecular mechanics force fields.

  • Steered Molecular Dynamics (SMD)
  • Potentials in ab-initio methods
  • Hybrid QM/MM
  • Protein Folding
  • Enzyme catalysis
  • Protein stability
  • Molecular recognition of proteins
  • DNA and membrane complexes

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