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

update info on NAMD #5

Open
orbeckst opened this issue Dec 4, 2024 · 5 comments
Open

update info on NAMD #5

orbeckst opened this issue Dec 4, 2024 · 5 comments
Assignees

Comments

@orbeckst
Copy link
Member

orbeckst commented Dec 4, 2024

The NAMD section in the README should link to @amruthesht 's repo with the patch and explain the steps for getting NAMD3 + IMDv3.

@HanatoK
Copy link

HanatoK commented Dec 5, 2024

Hi! I have made a merge request in the NAMD repository with @amruthesht 's patch, and adapted NAMD's code to support IMD in the GPU-resident mode. Please see NAMD's merge request if you can access NAMD's repo: https://gitlab.com/tcbgUIUC/namd/-/merge_requests/359 (or the branch in https://gitlab.com/tcbgUIUC/namd/-/tree/feature_imdv3). It would be better if you could review and test the NAMD merge request.

The NAMD demos should be updated, too. I think the lines in https://github.com/ljwoods2/imd-workshop-2024/blob/main/namd-demos/distances/distance-demo.ipynb and

from imdclient.IMDREADER import IMDReader

should be changed to

from imdclient.IMD import IMDReader

and the IMD port should be changed to 9918 to match the NAMD configuration.

@orbeckst
Copy link
Member Author

orbeckst commented Dec 5, 2024

Thanks a lot @HanatoK !!

I raised #6 for the specific problems with the materials. Thanks for raising them.

@ljwoods2
Copy link
Collaborator

ljwoods2 commented Dec 5, 2024

Hi @HanatoK, thank you for the contribution!

How can we request access to the NAMD github repo?

@amruthesht
Copy link
Collaborator

@HanatoK the changes to the namd-demos have been in a seperate branch. They will be merged into main shortly.
Thank you again for reaching out after the workshop!

@HanatoK
Copy link

HanatoK commented Dec 5, 2024

@ljwoods2 You need a Gitlab user account, follow the guide in https://gitlab.com/tcbgUIUC/namd, and then fill the request form in https://www.ks.uiuc.edu/Research/namd/gitlabrequest.html. David Hardy from the NAMD developer team will enable your access to the NAMD Gitlab repo.

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

No branches or pull requests

4 participants