Comments (5)
@faranak1991 could you please paste your conda environment (conda list
)? For the second error, I have a feeling you may need to downgrade pint to 0.20.1, with something like conda install -c conda-forge pint==0.20.1
or pip uninstall pint && pip install pint==0.20.1
.
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Thank you for your reply @lilyminium. The error was resolved by installing the specific version of Pint. Additionally, I have provided the list of packages installed in the Conda environment in attached file.
Regarding tutorial02, the "estimated_data_set.json" file does not show the properties as expected, it appears as:
{
"@type": "openff.evaluator.datasets.datasets.PhysicalPropertyDataSet",
"properties": []
}
Do you have any recommendations or advice regarding this?
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That indicates something went wrong earlier in the tutorial when estimating properties. There should be some error messages a few cells up indicating something crashed or possibly didn't start.
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Thanks @mattwthompson . I see that certain properties have already been specified as follows. Is there any possibility to include transport properties such as viscosity in the existing set?
Also, does the openff-evaluator accurately estimate these new properties?
(particularly for a molecule with 44 atoms)
<class 'openff.evaluator.properties.binding.HostGuestBindingAffinity'>
<class 'openff.evaluator.properties.density.Density'>
<class 'openff.evaluator.properties.density.ExcessMolarVolume'>
<class 'openff.evaluator.properties.dielectric.DielectricConstant'>
<class 'openff.evaluator.properties.enthalpy.EnthalpyOfMixing'>
<class 'openff.evaluator.properties.enthalpy.EnthalpyOfVaporization'>
<class 'openff.evaluator.properties.solvation.SolvationFreeEnergy'>
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The supported properties are just what are available in the API right now; PRs for others would be welcome.
Evaluator has been used to accurately, we believe, compute those properties in a handful of studies. It's hard to say it'll work for every molecule of a particular size, but any system suitable for equilibrium MD will likely work fine.
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Related Issues (20)
- Random halting of estimations (experiments/solvent2.nc) HOT 5
- Solvation free energy calculations failing HOT 10
- Loosen MDTraj constraint HOT 3
- tutorial data and script are outdated HOT 1
- unit bug forcebalance 1.9.4 + evaluator 0.4.1 + toolkit 0.11.4 in tutorial04 HOT 5
- Virtual sites missing from gradient calculations HOT 8
- Remove modules depending on Yank
- OpenMM 8 causing test failures HOT 2
- Star imports misconfigured HOT 1
- Unit-related AttributeError on code which previously worked HOT 6
- FilterBySmirks does not work with isotopes HOT 6
- Remove use of `pkg_resources`
- Pandas 2 breaks things HOT 3
- OE_LICENSE HOT 3
- unit HOT 16
- Pint removed upcast_types = [] from pint.compat HOT 3
- openff-evaluator conda installation problems HOT 3
- Update calls to Simulation.MinimizeEnergy to provide tolerance as force, not energy HOT 4
- tutorial04 - No module named 'forcebalance' HOT 1
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