CLI settings and assorted clean up - #329
Merged
Merged
Conversation
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
|
|
jthorton
commented
Sep 25, 2026
| for repeat in {0..2}; do | ||
| jobpath="network_setup/transformations/${dirpath}_${repeat}.job" | ||
| cmd="openfe quickrun $file -o results/repeat${repeat}/$relpath -d results/repeat${repeat}/$dirpath" | ||
| cmd="openfe quickrun $file -o results_${repeat}/$relpath -d results_${repeat}/$dirpath" |
Contributor
Author
There was a problem hiding this comment.
This can be reversed but I was trying to standardise how we recommend formatting the results output.
IAlibay
reviewed
Sep 25, 2026
| "- [Absolute hydration free energy calculations](https://docs.openfree.energy/en/latest/tutorials/ahfe_tutorial.html)\n", | ||
| "- [Molecular Dynamics (MD) simulations](https://docs.openfree.energy/en/latest/tutorials/md_tutorial.html)\n", | ||
| "- [Absolute binding free energy calculations](https://docs.openfree.energy/en/latest/tutorials/abfe_tutorial.html)\n", | ||
| "- [Relative binding free energy calculations using a Separated Topologies (SepTop) approach](https://docs.openfree.energy/en/latest/tutorials/septop_tutorial.html)\n", |
Member
There was a problem hiding this comment.
Can you sort this alphabetically please? I.e. we want the absolutes together
IAlibay
approved these changes
Sep 25, 2026
IAlibay
left a comment
IAlibay
left a comment
Member
There was a problem hiding this comment.
Just the one thing, but I'll approve early
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.