Skip to content

Commit

Permalink
Add question to FAQ about sending a system to HPC (#1925)
Browse files Browse the repository at this point in the history
* Add question to FAQ about transferring a prepared system

* Update changelog

---------

Co-authored-by: Jeff Wagner <[email protected]>
  • Loading branch information
Yoshanuikabundi and j-wags authored Aug 12, 2024
1 parent d91b8f2 commit 6a1c6a2
Show file tree
Hide file tree
Showing 2 changed files with 10 additions and 0 deletions.
9 changes: 9 additions & 0 deletions FAQ.md
Original file line number Diff line number Diff line change
Expand Up @@ -175,3 +175,12 @@ Constraints can be removed from bonds involving hydrogen by removing the corresp
```python
del forcefield['Constraints']["[#1:1]-[*:2]"]
```

## How can I transfer my prepared system to HPC resources for simulation?

OpenFF recommends exporting a prepared `Interchange` to the target MD engine and using the MD engine's recommended method to transfer it to HPC resources. This way, no additional dependencies need to be installed on the HPC resource to use OpenFF tools during preparation. For most MD engines, simply transfer the files produced by the appropriate [`Interchange.to_*()`] methods. For OpenMM, create a `System` Python object with [`Interchange.to_openmm_system()`] or [`ForceField.create_openmm_system()`] and transfer it by [serializing to XML].

[`Interchange.to_*()`]: https://docs.openforcefield.org/projects/interchange/en/stable/_autosummary/openff.interchange.Interchange.html
[`Interchange.to_openmm_system()`]: https://docs.openforcefield.org/projects/interchange/en/stable/_autosummary/openff.interchange.Interchange.html#openff.interchange.Interchange.to_openmm_system
[`ForceField.create_openmm_system()`]: https://docs.openforcefield.org/projects/toolkit/en/stable/api/generated/openff.toolkit.typing.engines.smirnoff.ForceField.html#openff.toolkit.typing.engines.smirnoff.ForceField.create_openmm_system
[serializing to XML]: https://openmm.github.io/openmm-cookbook/latest/notebooks/cookbook/Saving%20Systems%20to%20XML%20Files.html
1 change: 1 addition & 0 deletions docs/releasehistory.md
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
### New features

### Improved documentation and warnings
- [PR #1925](https://github.com/openforcefield/openff-toolkit/pull/1925): Adds a FAQ entry describing how to send a prepared system to HPC resources.


## 0.16.3
Expand Down

0 comments on commit 6a1c6a2

Please sign in to comment.