Molecular Dynamics

Technology: Both AMBER and GROMACS molecular dynamics suites are available

Molecular dynamics simulations are useful for investigating the structures or interactions of molecules that are problematic to study using experimental techniques. MD is also useful for providing theoretical reaction pathways, estimating binding constants or providing a series of potential structures with which to compare to experimentally derived data.

Sophisticated computational calculations are used to simulate the forces that are present between atoms of a molecule, taking into account the various bonds that also exist as well as attractions or repulsions between charged groups. 

MD is particularly useful for biomolecules, such as small proteins, where it can be used to refine protein structures estimated from NMR data, to investigate the mechanisms by which small molecules therapeutics bind to a target, or simulate the effect of amino acid changes on protein structure.
Technical Detail
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