Molecular Dynamics simulation of a peptide in water



The movies (side view) show the adhesion mechanism of the peptide on the TiO2 anatase surface though classical MD simulation. The peptide backbone is shown as a green ribbon while the amino acids (the Arg3 and Asp 7) relevant for the adhesion mechanism are represented though CPK model. Only the interfacial water molecules are shown for clarity.
The hydrogen bonding network among them are displayed as white dashed lines. The hydrogen bonding network among the atoms of the peptide and those of the surface are shown in yellow dashed lines. MD simulation (15 ns, NVT ensemble, 300K) was performed with GROMACS v4.5.4 using OPLSAA force field for describing the protein and TiO2 parameters were supplemeted. Water molecules were modeled by single charge point (SCP) model. During the simulation the metal surface was kept frozen
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