Abstract
Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.
Highlights
If a molecular system is appropriately constructed, high-speed coarse-grained molecular dynamics (CGMD) simulations can be used with nearly the same accuracy as those achieved with All-atom molecular dynamics (AAMD) simulations
Vast computational power enables more accurate AAMD to simulate larger molecular systems for a longer time [35, 36], CGMD simulations are still good at handling large molecular systems, such as a membrane tether consisting of 4 million particles [37], a fully solvated protein in a liposome [38], and for effectively sampling the configuration space of target molecules because of rapid calculation speed
CGMD is a powerful tool for simulating molecular systems with large spatial and temporal scales, where chemical interactions are crucial
Summary
When used effectively, CGMD simulations can explain the physicochemical nature or even predict the behavior of a biological system, which may be impossible experimentally Because of this advantage, the amount of research that uses CGMD simulations has steadily increased in recent years (Figure 1). CGMD substantially reduces these costs by replacing multiple atoms with a larger, unified particle (coarse-grained atom); the degrees of freedom of a system are limited. This makes the energy function smoother and allows the use of larger time steps (e.g., 30 fs) as compared with that of AAMD (e.g., 2 fs). We describe specific examples of CGMD applications and the methods used to correlate the results obtained from simulations with those obtained from experiments
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