Molecular Dynamics

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.

Molecular dynamics simulations use super computer networks to perform many millions of calculations each second, by which they simulate the atomic forces that exist within and between molecules, taking account of the bonding structure - angles and dihedrals - and non-bonding interactions. A background forcefield is used, which provides a database of many potential bond strength/angles and the computer software will simulate atomic movements, typically over nanosecond timescales.

JBL Science have access to two MD software packages, each with its own forcefield. These are AMBER and GROMACS. Each gives somewhat different results and are useful for different types of calculations. We are happy to discuss your MD needs and determine which software is right for you.

The output of MD simulations are either static structures of molecules, or else simulated trajectories of the way that molecuar shape/interaction changes over the simulation time.

Simulations can be carried out under a variety of "conditions", such as inclusion of water and counter ions.

MD simulations work well for small molecules and biomolecules up to relatively small proteins, although the software remains unable to "fold" even the simplest proteins de novo - instead templates are used to provide starting points, from which simulations can be assumed to be accurate.

MD also works well for assessing binding interactions bewteen molecules or between proteins and small molecules. It is therefore useful for aiding structure-activity relationship investigations.

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