Expand gmxapi.modify_input use cases. - Redmine #3295
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
Use the output of one simulation segment as the input to
- 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.
- Replace coordinates or velocities in the simulation input.
A related issue should address convergence of
Some of the functionality and use cases may warrant expression in basic command line tools, but this has not been discussed much yet.