Lester Hedges
Lester Hedges
No problem. I'll look at that one to see if I can get it to fail.
No crashes yet, but I can confirm that I see the ligand "jump" after 50 frames. It almost looks like everything is slightly rotated within the box. It's visible for...
Could you try with `h_bonds_not_perturbed`? I found that `bonds_not_perturbed` would end up constraining everything for the `tyk2` set and I also couldn't run anything. (I think this was possibly due...
Just to check. Are you still using the `somd1` compatibility mode? All recent fixes are applied in that layer.
No problem. Thanks for confirming.
I've merged #226 into this branch so both PRs can be merged in one go.
This has now been updated with the latest commit from #226, i.e. the update to the equation used for the flat-bottomed distance restraint.
Just to add that I have also been seeing... ``` FATAL: exception not rethrown Aborted (core dumped) ``` about 50% of the time on interpreter shutdown on my `feature_emle` branch...
If you use the `return_as_system=True` kwarg to `d.commit()` then you can see that the underlying system (for the dynamics object) does still contain all of the frames, i.e.: ```python import...
Okay, this seems to fix it: ``` diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index cdb8a56b..965a67f9 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -1144,7 +1144,7 @@ class DynamicsData: from ..system import System if System.is_system(self._orig_mols):...