Dynamic Simulation Of RNA Molecule Based On GB - EMP Coarse - Graining Model

Francis Crick proposed the central dogma of molecular biology in1958from theimportance of the study of biological molecules began to gradually increase. With theadvances in computer technology, a variety of computer simulations of biomolecules methodshave been developed, and in many biomolecules research methods, molecular dynamicssimulation is the most mainstream methods. But because we studied molecular systems isgrowing, the use of all-atom model simulation corresponding analog time when getting longerand longer, in order to solve the whole problem of computational efficiency atomic model,this paper, a coarse-grained particle model.This article describes the coarse-grained model is an improved particle model, takinginto account that the charge asymmetry and their effects multiple moments shape, particleshape of the particles, coarse-grained model we used is based on particle shape asymmetryGay-Berne potential and expand the potential of the charge multiple moments built up. In thispaper we first build a model of three RNA molecules, in order to achieve accurate fitcoarse-grained model and all-atom model, we will be composed of four bases of RNAmolecules, ribose, and phosphate were constructed for the six coarse-grained particles.Select the basic idea of the respective parameter fitting, calculate their van der Waalsinteractions, atomic model by van der Waals interactions with the full comparison optimizedto obtain an atomic model of the whole nearer coarse parameter. After that, we carried onelectronegativity of various coarse particle analysis to determine the electrostatic interactionsites, fitting their electrostatic interaction parameters. Use GB-EMP parameters obtained toconstruct the corresponding RNA molecule coarse-grained model, and these three groups ofRNA molecules coarse-grained molecular dynamics simulation model. Fitting the root meansquare deviation coarse-grained model system, the radial distribution function parameters,and the parameters of the all-atom model were compared to the coarse-grained model tofurther optimize the parameters.Through a comparative analysis of various parameters of the resulting seen, althoughcoarse-grained model we constructed to meet the basic requirements of the simulation, but itsaccuracy can still be further improved. Establishment and Application of coarse-grainedmodel, significantly reducing the all-atom model dynamics simulation time and improve thecomputational efficiency advantages in computing time on this like DNA, the RNAmacromolecules such systems is particularly reflected.