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Molecular dynamics simulations are performed to study the physical mechanism of cobra cardiotoxin (CTX) proteins adsorption on alkanethiol self-assembled monolayers (SAMs) composed of S( CH2)5 CH3 and S( CH2)9 CH3. The binding energy of the CTX protein to the SAM surface of different mixing ratios of alkanethiol chains is calculated. The results show that the affinity of CTX to SAM reaches a maximum value when the ratio S(CH2)5 CH3: S(CH2)9 CH3 is 1:1, which agrees with the measurements of atomic force microscope obtained in Part I of our dual paper. Moreover, the binding energy is found to be linearly proportional to the CTX-SAM contact area. The hydrophobicity on CTX residues, the flexibility of SAMs and the behavior of water molecules near the SAM surface are examined to understand how these parameters affect the adsorption of a CTX protein on SAM surfaces. In addition, the importance of modeling water molecules explicitly in the study of protein adsorption is demonstrated by applying different solvent models.