Molecular Dynamics Simulations Of DNA Based On GB-EMP Coarse-Grained Model

Molecular dynamics has became an important simulation tool which is used inresearching complex molecular systems. But the all-atom molecular mechanics model isprohibitively expensive and time-wasting, and the capacity of computers is needed to beimproved. So molecular dynamics simulation still has some limitations for the system ofbiological macromolecules. And the coarse-grained model which is mentioned in this papercan overcome these defects.The coarse-grained model which is mentioned in this paper is improved compared withthe original coarse-graining model. Considering the anisotropic shape and the electricmultipole effects of the CG particles, the coarse-grained model based on both the anisotropicGay-Berne potential and the electric multipole expansion which is including the charge, thedipole moment and the quadrupole moment is employed. Deoxyribonucleic acid (DNA) is notonly able to guide the development and vital functions of the biologies, but also an importantpart of biological research. The DNA molecule is the molecular compound which is made upof two chains based on the principle of complementary pairing. Firstly, two kinds of thedouble helix structure of the DNA molecule are constructed. Because of the DNA moleculesare macromolecules, DNA molecules are maked up of the deoxyribose, phosphate and fourkinds of bases. The six parts are simulated respectively in order to achieve the better results.Secondly, some elementary configurations for the six parts are selected. Then we calculate thevan der Waals potential of each configuration and obtain the GB parameters thoughcomparing the coarse-grained van der Waals potential with all-atom van der Waals potential inthe AMBER force field. In order to make the parameters of electric multipole potential moreaccurate, according to the electronegativity of each part, we select the different multipoleexpansion sites on the corresponding atoms and get the EMP parameters. Finally, using theGB-EMP parameters, we simulate the one selected DNA molecules in the coarse-grainedmodel. The results of root mean square deviation(RMSD), radial distribution coefficient,major groove width and minor groove width in coarse-grained and those in all-atom model fitquite well.In terms of the results, there are still some deviations between the results of thecoarse-grained model which we mention in this paper and the results of the all-atom model.We may get better results, if we adjust the location of the multipole expansion sites, add thenumber of the multipole expansion sites and debug parameters more accurate. Thecoarse-grained model is able to improve the speed of molecular dynamics simulation and still get the reasonable results. The advantage is more obvious especially for the macromolecularsystems. That is because the coarse-grained model ignores the vibration of bends, angles,dihedral angles, and uses the coarse-grained particles instead of the interaction between theatoms. Then the efficiency is greatly improved. Consequently, the coarse-grained modelwhich is used in this paper can be applied widely, no matter small molecular systems ormacromolecular systems.