Hi, I have created a model with 2 cholesterol molecules connected via a user defined bond between ROH atoms to mimic cholesterol on a scaffold.
I've added a PO4 molecule in between the ROH molecules. Ie the ROH-PO4-ROH bond. I've played around with the bond length and bond angle forces to mimic the system I want.
Is there something I should keep in mind about this system, especially when calculating free energy interactions?