Atomistic molecular dynamics (MD) simulations of a DNA double helix in the presence of either R3, R6 or R20 were performed using the Gromacs 5.0.7 software package. An effictively infinite dsDNA helix was made by placing a helix with sequence d(CG)10 in a simulation box of approximate dimensions 150 Å × 150 Å × 68 Å and binding the top and bottom of the helix across the periodic boundary condition along the z-axis. Either 40 R3, 20 R6, or 6 R20 chains were randomly added to respective simulation boxes, resulting in an N/P ratio of 3.0 in each system. Systems were solvated with ~ 48,000 TIP3P water molecules, and then, neutralized by randomly replacing water molecules with 80 Cl -ions. The parameters for DNA, arginine, water, and ions used in all simulations were the AMBER99 forcefield (AMBER99bsc0 for DNA and AMBER99sb-ildn-phi for arginine) subject to NBFIX corrections 65 that were downloaded from . Equilibration was performed using 5000 steps of steepest descent energy minimization followed by 100 ps of NVT simulation in which the system was heated from 0 to 300 K and 100 ps of NPT simulation at a pressure of 1 atm. The simulations were then continued for 100 ns of production simlation using an integration time step of 2 fs. Temperature and pressure were maintained at 300 K and 1 atm using the Nose-Hoover and Parrinello-Rahman schemes, respectively, with coupling constants of 2 ps. Long-range electrostatic interactions were treated with the particle mesh Ewald method using a 12 Å cut-off and 1.5 Å resolution grid. Interactions between DNA and arginine were analyzed during the final 50 ns of the simulations using analysis tools available in Gromacs . Arginine residues were defined as being in contact with the DNA when any atom of the residue was within 3 Å of any DNA atom, and a polyarginine chain was defined as being in contact with the DNA when any of its residues was in contact with the DNA. The Solvent Accessible Surface Area (SASA) of DNA was measured using the sasa command of Gromacs. We also defined a contact fraction for each arginine residue by dividing the number snapshots in which the residue was in contact with the DNA by the total number of snapshots analyzed. Simulation systems were visualized using VMD 1.9.3