All of the organisms are made of cells. In the last recent decades, scientists and researchers study significantly on biological phenomenon. Deoxyribonucleic acid (DNA) as the most known biomolecule is interested by biologists and genetic engineers. DNA molecules is made of two nucleotide strand which is twisted to each other like a helix. For the special and unique structural properties of DNA, there are many research which is done on it not only in genetics but also in other fields like nanotechnology. For these reasons, predicting and describing DNA behaviors is crucial. So there are many models and simulations on DNA to help this purpose. In this work, first, we will introduce DNA as a biomolecule; then review some of particle simulation methods and study some DNA modeling like coarse-graining models. The purpose of this work is to calculate the forces on each parts of a DNA strand which is modeled by bead-spring model in the presence of a oscillating plate in a fluid. For this reason, we use LAMMPS code and SRD package to simulate fluid and DNA strand. So at first we simulate the fluid by use of stochastic rotation dynamics. Then we put an oscillating plate in our system to obtain velocity profile for the second stokes problem. In the next step we define a polymer strand by use of bead-spring model and attach it to the plate and calculate force on each bead.
