Hello, how to connect two molecules(dimer) through hydrogen bond? I try it, but when i use optimize geometry hydrogen bond break
It will depend on the force field you use. If you are using UFF, it does not include electrostatic or hydrogen bond terms.
If you use MMFF94 to optimize, it will form hydrogen bonds (e.g., try a cluster of water molecules).
Of course this will only work if you are using elements supported by MMFF94.
I am using MMFF94 for optimization, but the bond is also broken, I assumed that this is due to the cut-off radius I changed the properties of the hydrogen bond length (cut-off radius 3.6A instead of 2.5) and the hydrogen bond doesn’t break.
It’s normally decision? i afraid that isn’t pretty good