GROMACS version: 2024.1 (double precision)
GROMACS modification: No
I have attempted a steered MD into umbrella sampling simulation in which a thiolate anion sulfur (CYM residue) is restrained toward a nearby cysteine disulfide bond. This correctly results in the thiolate and one of the cysteines bonding to a target distance of around 2.1 angstroms, and a displacement of the alternate cysteine to around 2.8-3.1 angstroms. However, there is no free energy minima when performing the umbrella sampling for the new disulfide, with the potential steadily increasing across the reaction coordinate.
My question is therefore, is gromacs+CP2K capable of modelling this interaction (i.e. bond breaking between a disulfide and bond making between a thiolate and a cysteine)? There appears to still be an interaction pulling the disulfide bond together, and I am unclear of the cause as all relevant atoms should be included in the QM region. The QM region extends from the cysteine sidechains up to the Ca atoms and bound hydrogens
Any assistance would be greatly appreciated.
Many thanks