Two 100 ns NVT molecular dynamics simulations of dsDNA and dsRNA "GGGG" 18-mers (GCGGGGGGGGGGGGGGGC)

Supporting information for "Molecular origin of distinct hydration dynamics in double helical DNA and RNA sequences" by E. Frezza, D. Laage and E. Duboué-Dijon, J. Phys. Chem. Lett. 2024, 15, 4351–4358Two 100 ns-long NVT molecular dynamics simulation: one of dsDNA "GGGG" 18-mer (GCGGGGGGGGGGGGGGGC) and one of  the analogous dsRNA. The nucleic acid is explicitly solvated in water and neutralized with 0.15M KCl. Simulations were performed using the Gromacs 5 software. DNA is described with the Amber 99SB-ILDN force field with the BSC0 modifications, RNA is described with the Amber 99SB-ILDN force field with the BSC0 and χOL3 modifications, the SPC/E force field is used for water, and the Joung Cheatham paraeters for ions. The shared coordinates are saved every 500fs, twice less frequently than the original trajectories used for the publication, to reduce the size of the shared dataset below the allowed size limit.