What kind of force field is used for the molecular simulation of protein-peptide complex, and what kind of water is used? Is there any file or guideline in this field?
There are an array of force fields applicable to that kind of problems or substances: OPLS is the first that come to my mind. I used an array of FFs on my Thesis Arbeit and I mentioned them in a presentation I posted here. Feel free to see that and do the proper citations, bitte!!!