Metadynamics Sample Clauses

Metadynamics. Ab-initio molecular dynamics methods have been successfully applied during the last decades for different problems from materials science to biochemistry [21]. However, the main limitation of this approach is that it is still limited to processes occurring within a few tens of picoseconds. This will be particularly relevant if one is interested in studying chemical reactions, since these will usually not take place spontaneously on such a short time scale. Typically energy barriers of many kcal/mol need to be overcome. Several strategies have been developed to face this problem and the metadynamics method, introduced by Xxxx and Xxxxxxxxxx [22], appears to be one of the most efficient and robust solutions. The metadynamics method introduces a biasing potential in a collective variable space that influences the “real” dynamics. The collective variables selected to explore the configuration space of interest can be different parameters: from distances or angles to coordination numbers or the formation of a hydronium. The selection of the appropriate collective variables is a crucial point in obtaining accurate results with this technique. The biasing potential is built in such a way to disfavour the configurations already visited and to facilitate the exploration of regions of the configuration space that are statistically unlikely. In all the work presented in this thesis the history dependent potential is constructed as a sum of Gaussians, along distances as collective variables, according to