Hello, Gromacs community
A few months ago started using Gromacs but I only was able to perform an analysis with my protein and its ligand in a water system.
The issue is that now I want to perform an analysis with a complex conformed by my protein with a metallic ion (for example Zn2+) in a h2o2 or b-mercaptoethanol system. I mean using h2o2 or b-mercaptoethanol instead of water. All this to see if h2o2/b-mercaptoethanol affects the way that the metallic ion binds to my protein.
I don’t know if that’s even possible to do in Gromacs and if so, how could I perform that simulation
Hope you can help me answering this post.
Thank you in advance :)