Molecular dynamics simulations of DNA

Starting from an ideal B-DNA duplex structure for nucleotide sequence 5'-CGATTTTTTGGC-3' (complementary strand 5'-GCTAAAAAACCG-3'), the structure was placed in a periodic dodecahedron box, followed by the addition of 6691 water molecules and 25 mM NaCl, resulting in a charge-neutral system of 20868 atoms. Preparation of the system consisted of energy minimization and 1ns position restraint molecular dynamics, with restraints on the DNA heavy atoms. We used the AMBER03 force field to describe the interactions between atoms, in combination with the TIP3P water model. After equilibration, 5 200ns molecular dynamics runs at constant temperature (300 K) and pressure (1 bar) were initiated with different random inital velocities taken from the Maxwell-Boltzmann distribution at 300 K. The simulations were performed with GROMACS v4.5.3.