(i) To begin with, check if your MD simulations have been converged. One can use backbone RMSD as a starting point.

(ii) Once you are able to confirm the convergence, you may check if the ligand has any structural impact on your protein. For instance, secondary structure analysis would give you some idea here.

(iii) You may also want to check if your inhibitor has any H-bonding

(iv) Attempt to find out what other non-bonded interactions your inhibitor has with your enzyme at the binding site (https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/)

(v) You could measure the volume of your inhibitor binding pocket and see if inhibitor has increased or decreased the pocket volume

(vi) Backbone RMSF might be also useful to understand the residue flexibility of your protein

These are some of the preliminary ideas that you can explore in greater depth. If your protein has multiple chains and your inhibitor is located somewhere at the interphase then you may also explore inter-molecular interactions.

In addition to what Vishal Pandya wrote, you can try the following things as well:

• Principal component analysis to understand how essential motions change upon inhibitor binding. You can do it with NMWiz in VMD.
• Correlation analysis: You can check normalized linear mutual information or normalized dynamical cross-correlation analysis to see if/how certain domains/chains are affected by inhibitor binding. You can do it with https://github.com/tekpinar/correlationplus
• Centrality analysis: You can also investigate how some centrality metrics (such as betweenness, closeness, eigenvector etc.) are affected upon ligand binding. This can also be done with correlationplus.

Soundarya Priya I hope the attached link will be useful.

Article Structural insight into conformational dynamics of non-activ...