I am looking to run a simulation that models a protein in the presence of crowder. I have my system set up such that I have a protein structure centered in a box of water, however, I am unsure how to simulate crowding in this system (ie. by changing potential or inserting hard-spheres). Any direction on how to implement either method would be greatly appreciated.
A first suggestion from my side would be to add other proteins to your simulation. Adding a few ubiquitins, will still keep you well within reasonable system sizes for an MD simulation. Even if the time-scales you reach with such a larger simulation system might be short, this will allow you then to model the main effects of adding extra protein with much more precision than starting already out with a simplified model.
An alternative approach I know some people took were multi-scale simulations, where coarse-grain simulations are run along usual simulations.