Hello all,
I wonder if there is a way to calculate the free energy of a specific bond breaking/formation using the thermodynamic integration method. If yes, how should .mdp and .top files be modified?
Thanks,
Mohsen
Only if you have a reactive force field, which should then also be accurately parametrized. The practical answer is no in most cases.
Does it mean we cannot gradually disappear the bond to do TI?
You can make a bond disappear, but most force fields do not model the energy for bond breaking.
Is there any tutorial available for this in GROMACS?