Prof. Pep Español - FRIAS Soft Matter Seminar

Computer simulation of complex molecular systems can be carried out at different levels of detail, from a fully quantum mechanical description of  electrons and nuclei, through effective force fields between atoms and, at a more coarse level with the use of coarse grained entities representing many atoms as a unit. More detail implies obviously more computer resources, both in terms of memory and cpu time. Therefore, understanding how the different levels of description are connected is a major quest in recent times  in order to reduce  simulation costs and to access  larger systems and time scales.

A well established theory of coarse-graining indeed exists, although its practical implementation has been hampered by its daunting formality.  In the present talk, I will show how to convert this theory into a practical tool and illustrate the method by obtaining a coarse-grained description of big complex molecules in terms of the effective motion of its centers of mass. It will be apparent that the use of effective potentials between coarse molecules is only part of the story of coarse-graining. Any coarse-graining process has an inherent dissipation that in the present case is expressed in terms of friction forces between the effective molecules. This friction should be included in order to obtain a faithful representation of the molecular dynamics.