File:Conformation-and-dynamics-of-the-ligand-shell-of-a-water-soluble-Au102-nanoparticle-ncomms10401-s2.ogv

English: Supplementary Movie 1 The movie visualizes about 30 ns MD simulation of Au102(pMBA)44 in a 5nm3 cubic box filled with water molecules. In the visualization water is not shown. The simulation was done by using Gromacs version 4.5. The leap-frog Verlet integrator was used with time step of 2 fs. Other parameters are: a 1.0 nm Lennard-Jones cut-off with dispersion correction for energy and pressure, PME electrostatics with a 1.0 nm cut-off and 0.12 nm grid spacing, the velocityrescale thermostat with a reference temperature of 300 K and coupling time constant of 0.1 ps, and the Berendsen barostat with a reference pressure of 1 bar and coupling time constant of 1 ps. All bond lengths were constrained with the LINCS algorithm and no constraint was used for gold core. The movies contain 750 frames and the time between two frames is 40 ps. The colors of ligands are same as in Figure 6 in the main text. The coordinates of the full MD trajectory are given in Supplementary Data 1.