220110 rMD Meeting Protocol

[KRiedmiller]

Kimmdy Meeting:

Progress:

• Parsers: Top done, others in progress
• ParmEd works for small TOPs, not for bigger ones --> More work needed

ToDo:

• Housekeeping of file hist:
  • Clear responsibilities of file checking and writing to history
  • Deduplicate code in between tasks and reactions
• Different ways to change top:
  • Free Energy pertubation --> Eric after parameterization
  • Normal MD w/ restraints on not involved atoms
  • MD w/ small dt
• Look into intermolecular bonds:
  • Can have all necessary parameters
  • Alternative: Merge chains w/ crosslinks

Decisions:

• Include FF in top:
  • Would make changing parts quite easy
  • No issues w/ non-unique atomnames
  • ParmEd way of doing things
    • --> Needs to work with big files: Needs to be checked