I have completed my molecular dynamics (MD) on three complexes and protein alone. All the three complexes have Higher RMSD value than the protein alone. How can we justify this Higher RMSD of complexes. Thanks in advance.
Dear Mubashar Ilyas , check your RMSF plot to see whether residues have lower fluctuations in complex MD or not. You will get a better understanding if you dwell with RMSD and RMSF side by side.