OpenFreeEnergy / OpenFreeEnergy/openfe
[docs] we should point out some example(s) on how to read out the trajectories from our output files
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Description
@RiesBen
I checked again. State A is Valine and State B is Alanine. So, the ddg should be positive.
Also, I am wondering why the intermediates are needed in OpenFE if they are not used in perses and FEP+. I think FEP+ uses restraints on the backbone of the protein/peptide which may help with convergence. Is there a way to do the same with openFE to test if this is the source of convergence problems?
I think it would also be useful to visualize the trajectories. Are there any scripts available to extract trajectories from the saved simulation.nc file?
Originally posted by @amin-sagar in https://github.com/OpenFreeEnergy/openfe/discussions/889#discussioncomment-10214229
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Research direction
Start by reviewing the existing documentation and the saved simulation.nc output mentioned in the issue. Determine how trajectories can be extracted and visualized, then document a concrete example showing the process and expected result for users working with OpenFE output files.
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Assessment
- Tech stack
- python
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100