Short peptides (8 to 12 amino acids, no Cys) in aqueous solution bind selectively to nanoparticles composed of Au, Pd, or other nanoparticles depending on the sequence of amino acids. To elucidate the mechanism, we consider the two most strongly binding peptides (as evidenced by screening of several billion peptides using phage-display techniques) and two non-bonding peptides. The molecular reasons for binding versus non-binding and the specificity toward a certain surface are analyzed by molecular dynamics simulation of the peptides in solution and on the surface. First, we highlight the importance of force field parameters for metals and show that surface and interface energies for fcc metals can be reproduced with deviations of less than 10% compared to experiment, including metal-water interfacial energies, using simple LJ parameters. On even metal surfaces, the amount of polarization due to induced charges in the metal is found to be in the range 3 to 5 kcal/mol per dodecapeptide (12 amino acids), which is about an order of magnitude smaller than corresponding non-covalent binding energies. The analysis of the adsorption energies, changes in chain conformation relative to solution, Ramachandran plots, and orientational parameters provide first suggestions on the mechanism of binding to the neat metal surfaces, as well as to a Au-Pd bimetallic surface.