In principle you can do that. Question is, however, does it make any sense. You should keep in mind that MD is not very efficient in conformation search, in particular for protein-protein and protein-ligand complexes. In reality, MD is a tool to check the stability of a given/selected complex conformation.

In general, conformation search is very much influenced and hence limited by the multiple minima problem. For conformation search of complexes involving proteins a hierarchical approach is a much more promising approach. Walking down a distance scale one first should look at electrostatic surface pattern of both, protein and ligand because electrostatic interactions are the longest reaching ones. Thereafter one should look at topological compatibility. At the end, one should take into account local interactions because they are effective on comparatively short distances.

Thereafter, MD can be used to verify the stability. In a systematic way one should look for the response of the complex at different temperatures, even higher than 298 K. Of course, this is not a very quick approach but helps to minimize unwanted and misleading phenomena.

Thank you, sir. Is it alright if we consider the protein amino acids present within 10Ao radius surrounding the ligand for molecular dynamics. we are doing this due to the limitation of computation resources and the software is limited for 25000 atoms only.

Well, if you can exclude the existence of significant allosteric response of the protein, it is OK.

Thank you sir. You are lifesaver. Thank you so much sir.