Skip to content
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.

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

Add forcefield.py with library of FF options; include option to use united atom system #5

Open
wants to merge 8 commits into
base: main
Choose a base branch
from

Conversation

chrisjonesBSU
Copy link
Member

This PR achieves 2 things:

  1. Makes it a little easier to use difference force fields with the addition of forcefield.py. This essentially creates classes of different force fields that can be imported and passed into System.apply_forcefield rather than using foyer directly. The primary motivation for this was to add the opls force field that is slightly modified to work for PPS. I also included GAFF.

  2. I added a united_atom parameter that can be True or False when initializing the System class. If True, the hydrogen atoms will be removed, and the mass and charges of the heavy atoms they were bonded to will be be adjust to account for the lost hydrogens. This is all done in the apply_forcefield method. I think most of our simulations for this project can be UA, which will bump up our TPS performance.

To do:
Importing from the forcefield library in project.py doesn't seem to be working yet.

@review-notebook-app
Copy link

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.


Powered by ReviewNB

@chrisjonesBSU
Copy link
Member Author

After trouble shooting some issues with Marjan, we need to make the simulation workflow path more robust, we talked about making it a requirement that it is explicitly given

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant