Figure 2.

Superposition of the C_α traces of part of the HIV-1 protease x-ray structure 4phv before (dark line) and after (light line) 10 ps of MD simulation bound to the inhibitor (space-fill). The flap region (above the inhibitor) moved away from the x-ray structure during the simulation, with all-atom RMSDs of 0.54 Å at 0.1 ps, 0.95 Å at 1 ps and 3.30 Å at 10 ps, respectively. Generally, after 0.1 ps, as the all-atom RMSD increased, the correlation coefficient of the experimentally-determined and calculated binding energies decreased.