In the current study, GROMACS 5.0.4 software package was used to carry out all the molecular dynamics simulations. A total of two drug-DNA complexes were created keeping using the best docked poses obtained after docking for molecular dynamics simulations viz., (1BNA+ lig-1 and 1BNA+lig-2). A simulation for 5000ps was carried out for the studies of their dynamical behavior. There are many force fields proposed for the MD simulation studies of nucleic acids such as, CHARMM, AMBER, GROMOS, OPLS, ENCAD and BMS. Moreover, many studies have been performed regarding the comparison of force fields for the nucleic acids but AMBER force fields seem to be good for nucleic acid simulation due to the presence of specific topologies for the terminal nucleotides . During the current simulation, Amber03 force field, which was already embedded in GROMACS software suite, was used to generate the topology for the DNA sequence and antechamber module of AMBER program was used to generate topology of selected ligands through a python script: 'acpype.py' . The Ligand-DNA complexes were solvated in a box of different dimensions along the three axes using TIP3P water model at 298K . Sodium ions were then added to the solvated boxes containing the DNA-ligand complexes by randomly replacing the water molecules in order to neutralize the system, as the biological systems needs to be neutral overall before the production run begun. Particle Mesh Ewald (PME) was used to handle long-range electrostatic interactions under periodic boundary conditions . Energy minimization of the whole system was carried out in 25000 steps using Steepest Descent leap-Frog Integration Method followed by NVT ensemble equilibration at a constant temperature of 300K for 50s using Berendsen thermostat . The system was then equilibrated with NPT ensemble at a constant pressure of 1atm in 25000 steps using steepest descent leap-frog integrator . All the bonds involving hydrogen atoms were constrained using the LINCS algorithm . Graphs were plotted using XM-grace software . Variations in energies, Root mean square deviation (RMSD), root mean square fluctuations (RMSF), radius of gyration (Rg) and hydrogen bond distribution for each system was determined by the analysis of MD trajectories. The MD trajectories were visualized by means of VMD .