(color online) MD simulations of T7 RNAP at post-translocation state. (a) The crystal structure of T7 RNAP at post-translocation state. Different domains are depicted in different colors: fingers domain in orange, palm domain in green, thumb domain in yellow, and N-terminal domain in red. (b) Components near the active site. Amino acids are drawn with cartoon method in yellow, DNA and RNA strands are drawn with bonds method in purple and green, respectively. Residue Y639 is also drawn with bonds method. (c) Time series of root mean square deviation (RMSD) values of CA atoms of the whole protein in three trajectories with different initial velocities. (d) Root mean square fluctuation (RMSF) values of different CA atoms of the protein residues.