Global properties for molecular dynamics simulations.

<p>(A) The backbone atom root mean square deviation (RMSD) for apo, inhibitor bound, apo (truncated) and inhibitor bound (truncated) HCV NS3/4A protein, calculated with respect to the initial structure during the 100 ns molecular dynamics simulation. (B) Root mean square fluctuations (RMSF) of Cα for apo, inhibitor bound, apo (truncated) and inhibitor bound (truncated) HCV NS3/4A protein averaged over the simulation. (C) RMSD of the backbone atoms of residues 101–172 and 331–420 with respect to the first snapshot as a function of time.