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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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fix: create fake LJ bonds for #465

Closed KRiedmiller closed 1 month ago

KRiedmiller commented 2 months ago

Create LJ imitation Morse bonds for 1-3 and 1-4 interactions.

Tests still failing.

Edit: additional morse bonds bring additional exclusions with them, which we do not want. Better introduce more pairs.

Fixes #421

KRiedmiller commented 2 months ago

New solution creates changing pair interactions, and vanishing/growing morse bonds.

In gromacs, changing pairs was broken prior to version 23.2 (https://gitlab.com/gromacs/gromacs/-/issues/4769) Therefore, KIMMDYs minimum gromacs version would be 23.2. Given new gromacs versions are faster anyways, I'd say that's fine.

KRiedmiller commented 2 months ago

Integration tests running, coordinates tests need fixes