Veerbhan Kesarwani You may utilize tools for viewing and studying 3D protein structures, such as PyMOL, VMD, or Chimera, to examine the structural changes in a protein before and after molecular dynamics (MD) simulation. You may color code the changes in the structure by superimposing the protein structures before and after the MD simulation. You may also compute the root-mean-square deviation (RMSD) between the two structures, which provides a quantitative estimate of the differences between them. This may be accomplished with a variety of MD analysis tools, such as GROMACS, AMBER, or NAMD. Alterations in secondary structure, interactions between residues, and solvent-accessible surface area are other regularly used techniques to examine structural changes.

Thank you Qamar UI Islam.