Molecular dynamics simulation of anionic form of pentaglycine at pyrite–water interface was investigated on ideal and stepped (001) surfaces. In all cases, the adsorption occurs from carbonyl oxygens of the pentaglycine anion. The results show that the surface morphology and adsorption direction have significant effect on dynamic behavior of the system. According to the results of this study, tetrahedral carbons, amine nitrogens, and the hydrogens of pentaglycine have longer distance from pyrite surface in all cases in comparison with the carbonyl carbons and oxygens, thus are not influenced significantly by the surface morphology and adsorption direction. Direction of the adsorption along a- and b-axes (x- and y-directions) at ideal surface has no significant effect on adsorbate–adsorbent distance, but influences the radial distribution function of the carbonyl groups. Presence of the step shortens the adsorbate–adsorbent distance more than 5%. In addition, the step causes better solvation for pentaglycine anion. In all cases, the pentaglycine–solvent interaction is stronger than pentaglycine–pyrite interaction. As a final result, based on pentaglycine–pyrite surface distance, it seems that the pentaglycine is physisorbed on pyrite surface; thus, it can be concluded that the ideal and stepped (001) pyrite surfaces could not be suitable suggestions as catalyst for elongation of oligopeptides in “Iron–Sulfur World” hypothesis of Wachtershauser.