Skip to content

Fix cookbook rendering issues #173

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
atravitz merged 1 commit into from
Oct 22, 2024
Merged

Fix cookbook rendering issues #173

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion cookbook/bespoke_parameters_showcase.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@
"source": [
"# Recap\n",
"\n",
"So to recap the workflow can be reduced to the following steps:\n",
"So to recap the workflow can be reduced to the following steps:\n\n",
"- Plan the RBFE network\n",
"- Create a single SMIRNOFF style force field with all of the bespoke parameters for the network using the BespokeFit `combine` CLI\n",
"- Store the force field as a string in the OpenFE protocol under the `settings.forcefield_settings.small_molecule_forcefield` field\n",
Expand Down
2 changes: 1 addition & 1 deletion cookbook/user_charges.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
"\n",
"Unfortunately charge assignment can be both, a) time consuming for large molecules, and b) non-deterministic, especially when the molecule occupies a conformation far from a local minima in the AM1 energetic landscape. The latter can be particularly problematic as this can lead to significant differences in assigned partial charges between Protocol simulation repeats.\n",
"\n",
"To avoid these issues, we recommend applying `user charges` to `SmallMoleculeComponents`. In its simplest form, this is done by converting the `SmallMoleculeComponent` to an `OpenFF Molecule` calling the [OpenFF Molecule's `assign_partial_charges method`](https://docs.openforcefield.org/projects/toolkit/en/latest/api/generated/openff.toolkit.topology.Molecule.html#openff.toolkit.topology.Molecule.assign_partial_charges) and then re-loading it back into a `SmallMoleculeComponent` before further manipulation."
"To avoid these issues, we recommend applying `user charges` to `SmallMoleculeComponents`. In its simplest form, this is done by converting the `SmallMoleculeComponent` to an `OpenFF Molecule` calling the OpenFF Molecule's [assign_partial_charges method](https://docs.openforcefield.org/projects/toolkit/en/latest/api/generated/openff.toolkit.topology.Molecule.html#openff.toolkit.topology.Molecule.assign_partial_charges) and then re-loading it back into a `SmallMoleculeComponent` before further manipulation."
]
},
{
Expand Down