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OpenFreeEnergy/ExampleNotebooks
OpenFE vs FEP+ edge comparison

  • jthorton
  • Opened 
    23 days ago
  • #195

OpenFreeEnergy/ExampleNotebooks
colab notebook url install failing

condacolab s install_from_url() currently requires that the python version match their default version. This will make our install flaky, so I suggest we install using mamba instead so that we re more ...
  • atravitz
  • 4
  • Opened 
    on Feb 24
  • #193

OpenFreeEnergy/ExampleNotebooks
Cookbook for plotting when there are missing exp data

  • hannahbaumann
  • Opened 
    on Feb 13
  • #192

OpenFreeEnergy/ExampleNotebooks
add a `How to change water model notebook`

Is your feature request related to a problem? Please describe. !-- A clear and concise description of what the problem is. E.g. I m always frustrated when [...]-- Describe the solution you d like !-- ...
  • jthorton
  • Opened 
    on Feb 11
  • #189

OpenFreeEnergy/ExampleNotebooks
Fix lomap calls in notebooks

CI is failing when using lomap, update to the newest API.
  • jthorton
  • Opened 
    on Feb 11
  • #188

OpenFreeEnergy/ExampleNotebooks
protocol_repeats

Dear developper I created an input json file using the Python API, and then ran openfe quickrun to perform the RBFE calculation. I wanted to perform a short verification, so I set protocol_repeats = ...
  • satoshikanaoka
  • 3
  • Opened 
    on Jan 18
  • #186

OpenFreeEnergy/ExampleNotebooks
Change mapping defaults to allow for element changes

Partial follow-up from #https://github.com/OpenFreeEnergy/Lomap/issues/61 Our tutorials still encourage folks to disallow element changes in mappings. Now that we do element changes in practice we should ...
  • IAlibay
  • Opened 
    on Dec 18, 2024
  • #184

OpenFreeEnergy/ExampleNotebooks
add solvation details to showcase notebook

follow-up to https://github.com/OpenFreeEnergy/openfe/issues/1032#issuecomment-2517428723
  • atravitz
  • Opened 
    on Dec 4, 2024
  • #183

OpenFreeEnergy/ExampleNotebooks
Showcase notebook incorrectly says we can set box dimensions via the ChemicalSystem

Follow up from https://github.com/OpenFreeEnergy/openfe/issues/1032 Section 2.3 says that you can set the box vectors when creating a ChemicalSystem. As far as I m aware, this is incorrect. We should ...
bug
high-priority
  • IAlibay
  • 1
  • Opened 
    on Dec 4, 2024
  • #181

OpenFreeEnergy/ExampleNotebooks
User Guide review: execution

  • atravitz
  • Opened 
    on Nov 7, 2024
  • #178
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