[gmx-users] Limitations of simulations?

[Jonathan Saboury]

I just finished this tutorial and found it very informative:
http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf

However, This was based on a complex from a pdb.

I was wondering if it was possible to just simulate the protein without
complex and put the ligand as a solute and actually have it complex with
the protein. Obviously, if it could do this it would take a much longer
time than just simulating a complex, but if given enough time, could it
complex?

I have no formal experience with simulations and currently have no one
around me with enough knowledge on these topic to mentor me, so any help is
very much appreciated!

Thank you! :)