Year-end Sale % OFF 
Abstract
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink’s group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.
Highlights
Molecular dynamics (MD) is an extremely useful methodology to investigate the behavior of biomolecules and biomolecular systems and soft matter in general at a level of detail that is still inaccessible during experiments [1,2,3,4,5]
The friction and the stochastic force terms are taken from the Langevin equation [35], which is equivalent to the assumption that the fluctuating forces and the coarse-grained velocities are correlated only over an infinitesimally small period of time (δ-correlated); in other words, it is assumed that the fine-grained degrees of freedom move much faster than the coarse-grained ones
Because our study on the FBP WW domain and its mutants demonstrated that proteinfolding kinetics can be modeled reasonably by using MD with UNRES, we undertook an investigation of the effect of the non-diagonal friction tensor due to the solvent, which gives rise to the so-called hydrodynamic interactions (HIs), on the folding dynamics
Summary
Molecular dynamics (MD) is an extremely useful methodology to investigate the behavior of biomolecules and biomolecular systems and soft matter in general at a level of detail that is still inaccessible during experiments [1,2,3,4,5]. 17 years after Alder and Wainwright [1] had published the results of their first MD simulation, the reduction of atomistic representation of the system studies was attempted by Levitt and Warshell [11] This reduction is termed coarse graining (CG). The functional expressions are copied from all-atom force fields, which results in insufficient capacity to model the structures of the systems under study (e.g., protein structures). The reason for this is that the fine-grained degrees of freedom, not considered in CG models, can give rise to strong coupling between the coarse-grained degrees of freedom [24,25,26]. We discuss the applications of CG MD, illustrating them with examples from our research, and conclude by discussing possible directions of the developments of CG MD approaches
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
