effective generation of TPR files from MDP data

[eirrgang]

Sooner or later there needs to be something bundled with gmxpy to allow direct specification of MDP key-value pairs. The Beckstein gromacs-wrappers are okay, but not great. I can wrap the command line if I have to, but there is broad buy-in to do this. I will probably have to just borrow grompp and add Python bindings or CLI wrapper since it doesn't look like the migration of inputrec to gmx::Options will be complete soon. However, I could target gmx::Options and just migrate the parts of inputrec that are interesting to our use cases.

[peterkasson]

I think for this we want a few steps:

1. generate TPR files using MDP files
2. alter specific MDP key-value pairs
3. generate TPR files using a dict or similar

I'm not 100% sure we need step 3, but I think step 1 is high value and essentially binding grompp. Steps 1, 2, and 3 (optionally) would eventually co-exist.

[eirrgang]

This is part of a broad set of functionality: manage simulation parameters and inputs from Python

The following use cases warrant individual task issues that might be grouped into a "simulation input API" milestone spread across several development cycles:

• Manipulate an MDP data structure #52
• Create an input file (bind grompp code) #52
• API access to TPR data
  • read structure
  • read topology
  • read MDP data
  • change a parameter in a TPR file
  • write TPR data?
• provide simulation input by API
  • provide or amend structure and self-consistent topology
• modify molecular model
  • add / remove atoms
  • toggle atom types
  • set / remove other topological features
• modify force field parameters
  • generate or amend a structure and topology from atom typing / force field heuristics (limit scope: avoid atom typing logic and pdb2gmx-type tasks; just consider generating topologies for provided structure with provided force field parameters)