GROMACS version: 2018
GROMACS modification: Yes/No
I have two MD simulated systems of enzyme; free enzyme and the enzyme with a metal ion. I generated RMSD plot using gmx commands but the plot does not show any significant difference for the enzyme in the two situations. Then I found that we can calculate the hydrogen bond order parameters using RMSD analysis. But how can we do that?
PS; If there is no significant difference in RMSD plot for enzyme in two situations, does that mean there is no effect on the enzyme with the presence of metal ion?