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graeter-group / kimmdy

Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)
https://graeter-group.github.io/kimmdy/
GNU General Public License v3.0
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pairs refer to 1 - 4 interactions, need to find the pairs for a bond 2 - 3 #52

Closed jmbuhr closed 2 years ago

jmbuhr commented 2 years ago

https://github.com/hits-mbm-dev/kimmdy/blob/4cde37430db18b4c6e680ec84471efec2725647c/src/kimmdy/changemanager.py#L29-L33

ehhartmann commented 2 years ago

When changing the topology, I construct pairs by iterating through all dihedrals and taking the first and fourth atom as pairs. As the dihedral list is complete (all possible proper dihedrals should be in the topology), this should include all pairs. For this problem, we could go through all dihedrals and check whether the breakpair is at the position 2 and 3 of the dihedrals to find pairs that we need to remove.

ehhartmann commented 2 years ago

Likely solved from the topology branch merge