touchpoint_19 Aug 2025

Agenda

1. Housekeeping and review TODO (15 mins)
2. Resume github meeting minutes management
3. Implement example notebook for water-ibuprofen interface - Mike

• BMS team will test out the interface notebook. Once the teething issues are ironed out, we can add the code to the API: Action Item #2
• Mike to merge in the code into main: Action Item #1

1. Dodecahedron simulation box issue with visualization – test on Lai molecule - Mike

• Test xtc file format: Action Item #3

1. Implement shrink step for packing – add it into the notebook for multi mAb example - Mike

• Mike packed a 3 mAb system. Need to handle stability. Will experiment with ramping up pressure. Will also evaluate packing and shrinking the un-solvated system. However, we may need to apply an implicit water model to avoid instability: Action Item #4

1. Review the longer simulation for mAb – Steven

• Steven will run the longer simulation: Action Item #5
• Code for dcd output is here: https://github.com/omsf/OpenPharmMDFlow/blob/feat/test-new-pdb-loader/experiments/new-pdb-loader/opennmm-mab-1.py

1. Try creating random packing water-ibuprofen-CAP-trimer - Dipak

• In progress: Action Item #6

Attendees

1. Mike
2. Stephen
3. Steven
4. Dipak

Meeting notes

Action Items

1. Ask if nvidia container runtime is available so that the docker images can access the GPU. Can I pass in the docker image uri, can the environment start up with the image? - Stephen
2. Build a test docker image to test the workflow using Docker - Mike
3. Assign partial charges to the CAP polymer using naggle - Mike