update info on NAMD

[orbeckst]

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

[HanatoK]

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]

Thanks a lot @HanatoK !!

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

[ljwoods2]

Hi @HanatoK, thank you for the contribution!

How can we request access to the NAMD github repo?

[amruthesht]

@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]

@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.