Note first that indeed the cMD simulation only binds the protein in a shallow metastable precursor state, from which it cannot escape in the 20 ns run; aMD, in contrast, allows for a steady decrease 
of the binding energy, as the protein continuously changes conformation and acquires deeper bound states. This figure also demonstrates that the number of time steps simulated in this study, 1:107 appears sufficient to estimate the final adsorption energy to be around 800 kcal/mol. This is a factor of 7{8 larger than the cMD simulations predict. Note finally that orientation 1 achieves a better binding than orientation 1, see our discussion of Fig. 4 below. The protein, in the case of aMD, has AbMole Ellipticine spread completely on the graphite surface and forms a flat peptide monolayer. This can be confirmed by the temporal evolution of the radius of gyration. Here, orientation 2 has spread more, both for classical and accelerated MD. The reason hereto is that the molecule has more flexibility in this orientation for spreading out on the surface due to weaker van-der-Waals interactions formed in the early adsorption stage until 2:106 time steps; this feature has already been discussed in our previous work. Interestingly, both orientations in the case of aMD show the same secondary structure content after adsorption as can be seen in Table 1. It seems that after 20 ns of accelerated MD simulation using the above mentioned boost parameters the final unfolded adsorption state has been found. When comparing aMD and cMD one can clearly recognize that the helical and b-sheet content is only slightly reduced in classical simulations. Even during the 100 ns simulation there has not been a great reduction in the b-sheet content while one can recognize fluctuations in the helical content comparing with the 20 ns cMD simulation of orientation 2. On the other hand, accelerated simulations show almost no remaining secondary structure except one small 310-helix. This finding of denaturation is in agreement with other adsorption studies on hydrophobic graphite surfaces. As can be seen in Fig. 3 b topologically distant protein strands show a roughly parallel arrangement which is believed to result from graphite’s hydrophobicity, crystallinity, and smoothness and the optimized intramolecular interactions. This phenomenon of unfolded proteins with parallel strands was observed experimentally; this agreement demonstrates that aMD provides reasonable adsorption structures. Additionally, we performed cartesian principal component analysis to identify the conformational space during protein adsorption. In this case, the trajectory was projected onto the first two eigenvectors of the protein atom covariance matrix which account for the largest internal motions of the protein. From these results we can clearly conclude that aMD provides considerably improved sampling of the conformational space. This result is in agreement with the findings of investigations using aMD in other applications. Especially in the case of orientation 2 very large conformational motions could be identified.