Open ehhartmann opened 2 months ago
Good point. We just have to check if removing this can lead to us trying to break already broken bonds.
There are two ways to go about this, having a maximal plumed file with everything ever necessary and never deleting from it, or one in sync with the topology. When we scale to many reactions, option 1 might become unfeasible, also it can slow down the expensive part, the MD. 2 is more complex to implement.
At the moment we automatically remove plumed variables from the plumed file if a bond is broken. This is the behavior we want if we only do homolysis but for homolysis/recombination simulations or something else, we might not want to remove the plumed variables.
https://github.com/hits-mbm-dev/kimmdy/blob/cf625b2239838f40ec3dcc6b86240f57a8258957/src/kimmdy/runmanager.py#L764-L768
Not calculating homolysis rates for broken bonds can also be solved in the homolysis plugin and is a config option at the moment.
What do you think about removing the
break_bond_plumed
call?