2024-03-10/11 Mitchell/Wagner Check-in meeting notes

• PDB to simulation

  • JM – Could make this even shorter

• Vsites

  • Monovalent geometries look funny, JM will report to MT

  • For final visualizations, just do one mol that exhibits multiple vsite types

• Micelle

  • Pre-charge lipid and distribute as SDF

• RNA

  • PDBFixer isn’t neutralizing, since it doesn’t understand the phosphate group charges. JM will make it a red example.

• General

  • Do OMP_NUM_THREADS in terminal instead of notebooks

  • Colab won’t let you do multiple notebook files with one env - Will need to have them concatenated

2024_03_11

• PDB-to-simulation

  • Added in a minimizeEnergy call

• QC interface

  • JM will pre-execute this one

  • For next run, could show sulfonamide problems resolving with openff-2.2

• RNA

  • PDBFixer isn’t neutralizing, since it doesn’t understand the phosphate group charges. JM will make it a red example.

  • For next run, could include some lipids

• NCAA

  • For next run, could do comparison of FF14SB charges to NAGL.

  • For next run, could do a bigger protein

• JM will make a concatenated version for colab.

  • JM – I can’t vouch that these will all run on colab, one or two might crash

  • JW – That’s fine, I wouldn’t worry about that.

• JM will post materials by end of his workday

• JW will send out reminder emails tomorrow morning (~14ish hours from now)

• 
  
  

• JM – We could use a new simulation setup pipeline.

  • JW – Some overlap with a possible roadmap goal (simulate >>50% of PDB), I’ll pass this on.