Abstract
In the last few decades, computer simulations have become a fundamental tool in the field of soft matter science, allowing researchers to investigate the properties of a large variety of systems. Nonetheless, even the most powerful computational resources presently available are, in general, sufficient to simulate complex biomolecules only for a few nanoseconds. This limitation is often circumvented by using coarse-grained models, in which only a subset of the system’s degrees of freedom is retained; for an effective and insightful use of these simplified models; however, an appropriate parametrization of the interactions is of fundamental importance. Additionally, in many cases the removal of fine-grained details in a specific, small region of the system would destroy relevant features; such cases can be treated using dual-resolution simulation methods, where a subregion of the system is described with high resolution, and a coarse-grained representation is employed in the rest of the simulation domain. In this review we discuss the basic notions of coarse-graining theory, presenting the most common methodologies employed to build low-resolution descriptions of a system and putting particular emphasis on their similarities and differences. The AdResS and H-AdResS adaptive resolution simulation schemes are reported as examples of dual-resolution approaches, especially focusing in particular on their theoretical background.
Highlights
Since the pioneering work carried out by Berni Alder [1] in the 1950s, in silico experiments, such as Molecular Dynamics (MD) or Monte Carlo (MC) simulations, allowed researchers to obtain major advancements in the understanding of systems with many degrees of freedom
The Adaptive Resolution Scheme (AdResS) represents the first effective and computationally efficient method to simulate a system where two different models, e.g., an all-atom one and a coarse-grained one, are simultaneously employed in different subregions of the simulation domain, interfaced in such a way to allow molecules to freely diffuse from one region to the other
In the adaptive resolution simulation (AdResS) setup, on the other hand, finite-size effect can be neglected for sufficiently large boxes, allowing one to characterize the response of the system’s properties in a small subregion when atomistic interactions with the bulk are switched off, but the thermodynamics is the same as in a fully-atomistic simulation
Summary
Since the pioneering work carried out by Berni Alder [1] in the 1950s, in silico experiments, such as Molecular Dynamics (MD) or Monte Carlo (MC) simulations, allowed researchers to obtain major advancements in the understanding of systems with many degrees of freedom. For example, certain solvated (macro)molecules, active sites of enzymes, the interaction of specific polymer ends at a surface, or a small spherical region in a homogeneous fluid whose radius is of the length scale of the property we are interested in For such systems the remaining, “non-interesting” region consists of the volume containing all those degrees of freedom which will be eventually neglected and/or discarded once the simulation is done, such as the solvent or large parts of a macromolecule which do not play an active role in the process of interest (e.g., all atoms sufficiently far from the active site of an enzyme). Physics”, 2013 [36]), as well as on original publications on the respective methodologies [33,34,37,38,39,40]
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