Coarse-Grained Molecular Dynamics

The book entitled Coarse-Grained Molecular Dynamics Simulations provides an overview of the most used coarse-grained (CG) techniques and their applications on different systems. The CG methods offer results for larger systems over a long period of time that are not obtainable with the all-atom description of these systems. The thermodynamics-based, structural-based and force matching methods for constructing potentials, used in the building of effective CG models, are discussed in the first part of the book. In this part also is highlighted some significant application of the coarse-grained molecular dynamics simulations in biochemistry and medicine. The rest of the book gives a detailed description of different CG models, constructed for specific molecules and systems. Proteins and peptides, topic of part 2 of the book, are scientifically interesting objects, as well as, for their medical importance as potential drugs. Most of the current docking procedures are focused on all-atoms conformational adjustments and fail to reproduce large-scale protein motion. CABS-dock, which employs a coarse-grained representation of proteins, is one of the very few tools that allow unrestrained docking with large conformational freedom of the receptor. Another CG technique used for a description of protein folding and dynamics is the G?-like model in which each amino acid residue is represented as a single unified atom, and either an attractive or a repulsive interaction is defined between any two residues. In this part of the book are also shown interesting investigations of interactions of proteins with lipid bilayers on CG level. Computer modelling of very large bimolecular systems, such as long DNA and RNA cannot reach the all-atom resolution in a foreseeable future and this necessitates the development of CG approximations. Part 3 of the book present different CG models used for prediction of structures, solution properties and dynamics of DNAs and RNAs. The last part of the book, Coarse-Grained Models for Lipids, collect a big selection of researches in the area. The fundamental building blocks of all cell membranes are phospholipids. Phospholipid molecules can demonstrate more than one micellar structures, which play important role in drug delivery systems as well as in biological systems. The use of CG models in exploring a variety of structural and dynamic properties of large molecular systems built from lipid molecules is discussed in details. The CG-MD technique can provide a good approximation based on the selection of the interaction parameters, as well as filling the gap between theoretical and experimentally determined results. Although CG-MD has provided valuable information for understanding the different phenomenon, there is still limits in its application, but the continuous theoretical developments guarantee the fast progress of this area.