I am in the process of running alchemical free energy simulations. I just came across YANK in my search. From the manual, it seems to be an excellent platform for my needs. However, a part of my research plan is to conduct simulations in a mixed solvent (water and methanol). I'm wondering if a mixed solvent system can be prepared using YANK? I tried to look at the manual but couldn't find a way to prepare a mixed solvent environment.
Any suggestions would be appreciated