Protocol for molecular dynamics of d G 7 quadruplex structures

Molecular dynamics was performed at constant temperature with AMBER 4.1 all-atom force field [121] and Particle Mesh Ewald method (PME) was used for the calculation of electrostatic interactions [122]. This is a fast implementation of the Ewald summation method for calculating the full electrostatic energy of a unit cell in a macroscopic lattice of repeating images. The PME grid spacing was 1.0A. It was interpolated on a cubic B-spline, with the direct set tolerance set to 0.000001. Periodic boundary conditions were imposed in all directions. All solute-solute non-bonded interactions were calculated without jmy cut-off distance, while a non-bonded residue based cutoff distance of 9A was used for the solvent-solvent and for the solute-solvent interactions. The non-bonded pair list was updated every 20 steps and the 

SHAKE algorithm was applied to constrain the covalent bonds. A time step of 2 fs was used and the structures were saved after every 100 steps, i.e. at every 0.2 ps interval, for the entire duration of the MD run. 

---