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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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truncate_sim_files not robust #464

Open ehhartmann opened 2 months ago

ehhartmann commented 2 months ago

For rejection-free KMC it is not necessary to truncate trajectories. All we need to continue the run is a trr (and gro) file with the frame indicated by the recipe. For this we could use gmx trjconv -dump.

For rejection KMC/ extrande, we can keep the truncation as an option but the run should not fail if it doesn't work. This is just for analysis anyway.

KRiedmiller commented 2 months ago

gmx trjcat is the cause of the instability. Often it struggles when only a few frames are generated; in my experience, it becomes more stable with a double-digit number of frames or more.

I'd keep the current behavior for now, as it works with rejection and rejection-free KMC. Otherwise, the user has one more option to make a mistake without gaining a real choice.