Department of Bioscience and Nutrition
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The Molecular Modelling Group
From atomistic details to coarse-grained description
Biomolecular Modelling
Alessandra Villa
The basic challenge of simulation technique is one of describing the macroscopic (experimentally observable) properties of the system in terms of the interactions between atoms or group of atoms. The molecular system is described by a set of potentials (empirical force fields) based on simple chemical concept. That allows to define the potential energy of the system in terms of the coordinates of the atoms or groups of atoms. Newton equation of motion is used to predict the time evolution of the system.
It is important that the adopted model is capable of correctly describing and predicting the biological phenomena at corresponding spatial and temporal scale. The size and the time scale of some biological process can not be describe by atomistic models and necessitates the use of low-resolution models, so-called coarse grained models where several atoms are grouped into larger units. This approach allows not only to reduce the number of degrees of freedom in the simulation but also significantly to speed up the inherent timescale of the simulation.
