Lily Wang
Lily Wang
Running a plain `pip install` from GitHub or the downloaded repo results in the following message, which I believe is from an outdated version of versioneer: ``` Obtaining file:///Users/lily/pydev/physical_validation Preparing...
MDAnalysis is supposed to have force units of kJ/mol.A. **DL_Poly** [The DLPoly format seems to work in 10 J/mol.A ](ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf): > Last but not least, it is worth pointing out...
**Describe the bug** FYI: in the new version, the `PortalClient.modify_records` function looks for the old `new_tag`, `new_priority` kwargs and warns they're to be deprecated for `new_compute_tag`, `new_compute_priority`. However, the `BaseDataset.modify_records`...
**Describe the bug** If a property includes a molecule that is a recognisable amino acid, this will get named as such in Packmol. When that happens, the parameter assignment step...
**Describe the bug** A PreequilibratedSimulation workflow depends on sourcing from a file storage system (named `stored_data` by default) that contains equilibrated data. When `stored_data` is empty, running a PreequilibratedSimulation workflow...
I think I ran into a hopefully one-off error generating a PDB using the Equilibration workflow where not all bonds were present, so just opening an issue to collect any...
**Is your feature request related to a problem? Please describe.** I'm uncertain how public facing this kind of thing actually should be, but this has come up a couple times...
During equilibration, by default we simulate 200 ps at a time. This seems to take on the order of a minute. To check equilibration conditions, I usually set up conditions...
**Describe the bug** When working with a dataset of multiple properties, one can set off a benchmarking or fitting workflow where e.g. 80% properties succeed, but 20% fail. When this...
See https://github.com/openforcefield/openff-evaluator/pull/584#discussion_r2244495821_ For more context, when I adapt the test in `test_workflow.py` as below, it fails. This seems to only affect the `selection` filters, I'm not sure why. It goes...