Comments (5)
hannahbaumann
commented on July 30, 2024
1
I don't think I would put the results under network_setup since that seems confusing to me, but may just be me!
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RiesBen
commented on July 30, 2024
1
@IAlibay - file name of ligand_*json: ja my bad, I corrected that in the initial post
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IAlibay
commented on July 30, 2024
-----ligand_*json
Sorry for the silly question, but what is this? The alchemical network?
--results
I think the way we wanted to go was:
-- network_setup
- ligand_network.graphml
- alchemical_network.json
--transformations
--- transformation JSONs
-- results_0- replica 0 results for each transformation
-- results_1 - replica 1 results for each transformation
-- results_2 - replica 2 results for each transformation
- replica 0 results for each transformation
Does that match what you envision?
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IAlibay
commented on July 30, 2024
I don't think I would put the results under
network_setupsince that seems confusing to me, but may just be me!
Yes sorry! That should be separate
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IAlibay
commented on July 30, 2024
I've opened PR #76 with the aim of fixing this
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Related Issues (20)
- QA simulation instructions
- Document data retention policy
- Test post-simulation clean up script
- Document post-simulation clean up script
- Update front page instructions to reflect benchmark kickoff
- Notebook for visualizing the LigandNetwork graphml
- QA instructions for the quickrun call script
- Work out how we handle triplicate simulations HOT 4
- Fix number of frames being sub-selected in trajectory cleanup script
- Fix table of contents in docs
- Slack channel #consortium-advisory-board? HOT 2
- Update order of installation instructions
- Fix build warnings when building docs HOT 1
- Point to installation instructions from home page
- Update instructions to point to using conda-lock file with micromamba HOT 1
- Create a rough set of Maestro instructions for setting up systems
- Add protonation state check to PR template
- Update instructions for Private: Phase 1
- Write an analysis script
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