Molecular dynamics is a powerful tool for the characterisation in atomistic detail of solute conformation, interactions, dynamics and thermodynamics. Its application to flexible biomolecules in aqueous solution however is a challenging task given that the motions involved can be large and occur on time scales generally difficult to achieve with standard simulation methods. To improve sampling efficiency, we have introduced a modified molecular dynamics approach called swarm-enhanced sampling molecular dynamics (sesMD). Inspired by swarm intelligence algorithms, this method involves the cooperative interaction of a swarm of simulation replicas via a set of pairwise potentials incorporating attractive and repulsive components. We will describe the performance of the approach to enhance the conformational sampling of peptides, proteins and oligosaccharides in explicit solvent simulations. We will also discuss the potential of the sesMD method for computation of free energies within a thermodynamic integration framework.

Efficient molecular dynamics of biomolecules using a swarm-enhanced sampling scheme

252nd National Meeting (2016)

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