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Feature #3295

Expand gmxapi.modify_input use cases.

Added by Eric Irrgang 3 months ago. Updated 3 months ago.

Status:
New
Priority:
Normal
Assignee:
Category:
gmxapi
Target version:
Difficulty:
uncategorized
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Description

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.


Related issues

Related to GROMACS - Task #3256: Remove -nsteps option from mdrunNew
Related to GROMACS - Feature #3285: Run simulations from the same tpr file with different random seedsResolved
Related to GROMACS - Task #3014: gmxapi example Python scriptsIn Progress

History

#1 Updated by Eric Irrgang 3 months ago

  • Related to Task #3256: Remove -nsteps option from mdrun added

#2 Updated by Eric Irrgang 3 months ago

  • Related to Feature #3285: Run simulations from the same tpr file with different random seeds added

#3 Updated by Eric Irrgang 3 months ago

  • Related to Task #3014: gmxapi example Python scripts added

#4 Updated by Eric Irrgang 3 months ago

  • Target version changed from 2021-infrastructure-stable to 2021-refactoring

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