I was fortunate enough to attend a recent CP2K/GROMACS course and am now trying to test out the interface on some other toy systems. The reaction I’m trying to model is abstraction of the hydrogen from a carbon by an oxygen attached to a ferryl atom (I’ve attached a picture for the sake of clarity with the distance (reaction co-ordinate) between the two highlighted). Where I’m getting stuck in the generation of the initial conformations to pass onto the umbrella sampling protocol
Would I need to manually pull the hydrogen (i.e. change the co-ordinate) between the two or is there a more systematic way to do it? I appreciate for a dihedral-type problem I could use a strong pulling force in classical MD but this obviously won’t work for a bond-breaking type problem. Finally, for these types of calculations (where a bond involving hydrogen is being pulled), should I disable LINCS in GROMACS?
Many thanks for any help on this issue. Greatly appreciated.