GROMACS

This issue has a large component that is just documentation and testing, but the tracked issue may also be used to coordinate requests, feedback, and effort related to identifying and satisfying user requirements for modify_input() in gmxapi 1.0.

Use cases to be supported and/or documented, demonstrated, tested¶

• [ ] Override a simple simulation parameter, such as nsteps or ld_seed.
• [ ] Use the output of one simulation segment as the input to another.
  • Fork a simulation trajectory.
  • Perform replica exchange.
  • iteratively extend a trajectory.
• [ ] ... convert-tpr use cases...
• [ ] Override a non-trivial simulation parameter (requiring grompp reprocessing)
• [ ] Avoid writing many TPR files for similar simulations.

Meta¶

A related issue should address convergence of modify_input and convert_tpr code.

Some of the functionality and use cases may warrant expression in basic command line tools, but this has not been discussed much yet.