diff --git a/source/workshops/2024/protein_prep.md b/source/workshops/2024/protein_prep.md index 50742d74d..e32410b1f 100644 --- a/source/workshops/2024/protein_prep.md +++ b/source/workshops/2024/protein_prep.md @@ -5,14 +5,10 @@ Today, Jupyter notebooks are everything you need to prepare a molecular dynamics This workshop covers the preparation of a protein system from a structure downloaded from the PDB, entirely in the Jupyter notebook, complete with 3D visualizations at every step of the way. We hope to make it accessible even to new MD practitioners, assuming they have some familiarity with Python. First session -: [Feb 27 23:00 UTC](https://time.is/1000_28_Feb_2024_in_Canberra/Tokyo/Auckland,_New_Zealand/Los_Angeles/Chicago/Phoenix/New_York/UTC?Protein_Prep_OpenFF_Workshop) +: [Feb 27 2024 23:00 UTC](https://time.is/1000_28_Feb_2024_in_Canberra/Tokyo/Auckland,_New_Zealand/Los_Angeles/Chicago/Phoenix/New_York/UTC?Protein_Prep_OpenFF_Workshop) Second Session -: [Apr 17 12:00 UTC](https://time.is/2200_17_Apr_2024_in_Canberra/Beijing/Berlin/Los_Angeles/Chicago/Phoenix/New_York/London/UTC?Protein_Prep_OpenFF_Workshop) - -: [💨 Join on Zoom](https://us06web.zoom.us/j/85120722786?pwd=Hb4mp4gOkNnjyarG4RLsoR9ClEPDDC.1) - -Zoom links will be published here 24 hours before the sessions begin. +: [Apr 17 2024 12:00 UTC](https://time.is/2200_17_Apr_2024_in_Canberra/Beijing/Berlin/Los_Angeles/Chicago/Phoenix/New_York/London/UTC?Protein_Prep_OpenFF_Workshop) Materials and Google Colab links can be found below. diff --git a/source/workshops/2024/protein_prep/2024_protein_prep_workshop_materials.zip b/source/workshops/2024/protein_prep/2024_protein_prep_workshop_materials.zip index fe446df24..6a7d7dfa8 100644 Binary files a/source/workshops/2024/protein_prep/2024_protein_prep_workshop_materials.zip and b/source/workshops/2024/protein_prep/2024_protein_prep_workshop_materials.zip differ diff --git a/source/workshops/2024/protein_prep/colab-env.yml b/source/workshops/2024/protein_prep/colab-env.yml index 624d7d565..67a450f58 100644 --- a/source/workshops/2024/protein_prep/colab-env.yml +++ b/source/workshops/2024/protein_prep/colab-env.yml @@ -10,8 +10,8 @@ dependencies: - requests - packaging # Examples - - openff-toolkit-examples>=0.15.2 - - openff-interchange>=0.3.25 + - openff-toolkit-examples>=0.16.0 + - openff-interchange>=0.3.27 - openff-nagl >=0.3.7 # - openff-bespokefit # - openff-fragmenter diff --git a/source/workshops/2024/smirnoff.md b/source/workshops/2024/smirnoff.md index 1c30ac58b..9a51495f1 100644 --- a/source/workshops/2024/smirnoff.md +++ b/source/workshops/2024/smirnoff.md @@ -5,14 +5,10 @@ SMIRNOFF is an open format for specifying molecular mechanics force fields direc This workshop introduces the SMIRNOFF format to familiar MD practitioners and describes how a system can be parametrized from a SMIRNOFF force field for a number of different MD engines. We hope to get both users and developers of molecular mechanics force fields excited about this game changing format. First Session -: [Feb 20 23:00 UTC](https://time.is/1000_21_Feb_2024_in_Canberra/Tokyo/Auckland,_New_Zealand/Los_Angeles/Chicago/Phoenix/New_York/UTC?SMIRNOFF_OpenFF_Workshop) +: [Feb 20 2024 23:00 UTC](https://time.is/1000_21_Feb_2024_in_Canberra/Tokyo/Auckland,_New_Zealand/Los_Angeles/Chicago/Phoenix/New_York/UTC?SMIRNOFF_OpenFF_Workshop) Second Session -: [Apr 10 12:00 UTC](https://time.is/2200_10_Apr_2024_in_Canberra/Beijing/Berlin/Los_Angeles/Chicago/Phoenix/New_York/London/UTC?SMIRNOFF_OpenFF_Workshop) - -: [💨 Join on Zoom](https://us06web.zoom.us/j/87669037455?pwd=CK8ETt2HwXJe7h9rM42JbFzaU9RJFJ.1) - -Zoom links will be published here 24 hours before the sessions begin. +: [Apr 10 2024 12:00 UTC](https://time.is/2200_10_Apr_2024_in_Canberra/Beijing/Berlin/Los_Angeles/Chicago/Phoenix/New_York/London/UTC?SMIRNOFF_OpenFF_Workshop) Materials and Google Colab links can be found below. diff --git a/source/workshops/2024/smirnoff/2024_smirnoff_workshop_materials.zip b/source/workshops/2024/smirnoff/2024_smirnoff_workshop_materials.zip index 6f25ae5fa..b501fe137 100644 Binary files a/source/workshops/2024/smirnoff/2024_smirnoff_workshop_materials.zip and b/source/workshops/2024/smirnoff/2024_smirnoff_workshop_materials.zip differ diff --git a/source/workshops/2024/smirnoff/colab-env.yml b/source/workshops/2024/smirnoff/colab-env.yml index 89af46323..18c7fc1de 100644 --- a/source/workshops/2024/smirnoff/colab-env.yml +++ b/source/workshops/2024/smirnoff/colab-env.yml @@ -6,8 +6,8 @@ dependencies: - ipywidgets=7.6.0 - nglview=3.0.3 # Examples - - openff-toolkit-examples ~=0.15.2 - - openff-interchange ~=0.3.25 + - openff-toolkit-examples ~=0.16.0 + - openff-interchange ~=0.3.27 - openff-nagl ~=0.3.7 - openff-bespokefit - gromacs >=2021=nompi* diff --git a/source/workshops/2024/smirnoff/env.yml b/source/workshops/2024/smirnoff/env.yml index 275a864b5..4bf2063b0 100644 --- a/source/workshops/2024/smirnoff/env.yml +++ b/source/workshops/2024/smirnoff/env.yml @@ -13,8 +13,8 @@ dependencies: - black - isort # Examples - - openff-toolkit-examples ~=0.15.2 - - openff-interchange ~=0.3.25 + - openff-toolkit-examples ~=0.16 + - openff-interchange ~=0.3.27 - openff-nagl ~=0.3.7 - openff-bespokefit - openff-qcsubmit @@ -23,7 +23,7 @@ dependencies: - rich - jax - dgl - - nglview>=3.0.6 + - nglview>=3.0.6,<3.1.0 - xtb-python - pdbfixer - mdtraj diff --git a/source/workshops/2024/vignettes.md b/source/workshops/2024/vignettes.md index badef3f0e..04d890466 100644 --- a/source/workshops/2024/vignettes.md +++ b/source/workshops/2024/vignettes.md @@ -5,14 +5,12 @@ The OpenFF software ecosystem is a flexible and highly programmable collection o This workshop will display this flexibility by demonstrating a variety of unusual uses of the OpenFF ecosystem and its software neighbors. These "vignettes" will run the gamut from useful to cute, robust to experimental, and simple to complex. Rather than focus on the details of how each is accomplished, vignettes will each be demonstrated quickly alongside a brief highlight of the relevant part of the ecosystem. In the hands-on session after the prepared material, participants will be encouraged to investigate a thorny problem of their own with developer support. First session -: [Mar 12 22:00 UTC](https://time.is/0900_13_Mar_2024_in_Canberra/Tokyo/Auckland,_New_Zealand/Los_Angeles/Chicago/Phoenix/New_York/UTC?OpenFF_Vignettes_Workshop) +: [Mar 12 2024 22:00 UTC](https://time.is/0900_13_Mar_2024_in_Canberra/Tokyo/Auckland,_New_Zealand/Los_Angeles/Chicago/Phoenix/New_York/UTC?OpenFF_Vignettes_Workshop) Second session -: [Apr 24 12:00 UTC](https://time.is/2200_24_Apr_2024_in_Canberra/Beijing/Berlin/Los_Angeles/Chicago/Phoenix/New_York/London/UTC?Vignettes_OpenFF_Workshop) +: [Apr 24 2024 12:00 UTC](https://time.is/2200_24_Apr_2024_in_Canberra/Beijing/Berlin/Los_Angeles/Chicago/Phoenix/New_York/London/UTC?Vignettes_OpenFF_Workshop) -: [💨 Join on Zoom](https://us06web.zoom.us/j/87885784973?pwd=gnIHcbboXbxdopbG3OBb9kyoUKUYLr.1) - -Zoom links will be published here 24 hours before the sessions begin. +Materials and Google Colab links can be found below. ## Workshop Materials diff --git a/source/workshops/2024/vignettes/2024_vignettes_workshop_materials.zip b/source/workshops/2024/vignettes/2024_vignettes_workshop_materials.zip index 0daec3fbf..2e8140a8a 100644 Binary files a/source/workshops/2024/vignettes/2024_vignettes_workshop_materials.zip and b/source/workshops/2024/vignettes/2024_vignettes_workshop_materials.zip differ diff --git a/source/workshops/2024/vignettes/colab-env.yml b/source/workshops/2024/vignettes/colab-env.yml index 01155d5b4..11555159f 100644 --- a/source/workshops/2024/vignettes/colab-env.yml +++ b/source/workshops/2024/vignettes/colab-env.yml @@ -6,7 +6,7 @@ dependencies: - ipywidgets=7.6.0 # Examples - openff-toolkit-examples >=0.16.0 - - openff-interchange >=0.3.25 + - openff-interchange >=0.3.27 - openff-nagl >=0.3.7 - openff-bespokefit - openff-forcefields >= 2024.04.0