Each duplex was processed in two minimization stages, one heating stage, and two equilibration stages. For minimization stages, sander was used to perform energy minimization procedure with constant volume, periodic boundaries, and a non-bonded cutoff distance of 12.0 Å and 5000 steps of steepest descent followed by 5000 steps of conjugate gradient. For heating and equilibration stages, the non-bond cutoff distance was unchanged, the SHAKE algorithm was used to minimize the motion amplitude of hydrogen atom with a time step of 2.0 fs per step, and Langevin thermostat was used to control the temperature with the collision frequency of 1.0 ps -1 . The first round of energy minimization used a force constant of 100 kcal/mol Å 2 to constrain the DNA duplex. The second round of energy minimization was to minimize the energy of the entire system with the restraint removed. After the energy minimization, heating the optimized structure from 0 K to 310 K with a constant volume periodic boundary within 20 ps, and keeping the force constant of 10 kcal/mol Å 2 to constrain the DNA duplex. Then the system was allowed to equilibrate for 100 ps applying a constant pressure periodic boundary with constant pressure, a mean pressure of 1.0 atm and a temperature of 310 K. Using isotropic position scaling to maintain pressure with a relaxation time of 2.0 ps. Once the system reach equilibrium, using the same settings in the equilibrium state for running 5.0 ns simulations.