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Add simulation visualization notebook to how-to guides - #2344
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this looks good, but as mentioned over in OpenFreeEnergy/ExampleNotebooks#359, I think it would make sense to move the protocol-specific explanations over to the user guide. Thoughts? |
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@atravitz I added some of the content from the notebook to the protocol user guides here and removed it in the notebooks! |
* Update showcase assets * Look at showcase updates * Apply suggestion from @hannahbaumann
atravitz
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Nov 10, 2026
atravitz
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I think the content is good, but the single-paragraph format is confusing. I made a suggestion for making it more structured, but anything that makes it more readable is fine by me!
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| Each leg writes a multistate trajectory (``complex.nc`` and ``solvent.nc``) with its topology | ||
| (``alchemical_system.pdb``). The trajectory stores the positions of every replica, together with the λ state each | ||
| replica was in at each iteration. A trajectory can therefore be read in two ways: at a fixed λ **state**, combining | ||
| frames from whichever replica occupied that state, or along a single **replica** as it moves between λ states. | ||
| This applies to the default replica exchange sampler (``sampler_method = "repex"``). | ||
| With ``"independent"`` sampling, replicas never change state, so both give the same trajectory; | ||
| with ``"sams"``, a λ state is not necessarily occupied at every iteration, so reading by state may not be possible. | ||
| Only the atoms selected by ``output_indices`` are saved, which by default excludes water. | ||
| Both files can be loaded with `openfe_analysis`_ to visualize the simulation, extract the trajectories of the end states, |
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Suggested change
| Each leg writes a multistate trajectory (``complex.nc`` and ``solvent.nc``) with its topology | |
| (``alchemical_system.pdb``). The trajectory stores the positions of every replica, together with the λ state each | |
| replica was in at each iteration. A trajectory can therefore be read in two ways: at a fixed λ **state**, combining | |
| frames from whichever replica occupied that state, or along a single **replica** as it moves between λ states. | |
| This applies to the default replica exchange sampler (``sampler_method = "repex"``). | |
| With ``"independent"`` sampling, replicas never change state, so both give the same trajectory; | |
| with ``"sams"``, a λ state is not necessarily occupied at every iteration, so reading by state may not be possible. | |
| Only the atoms selected by ``output_indices`` are saved, which by default excludes water. | |
| Both files can be loaded with `openfe_analysis`_ to visualize the simulation, extract the trajectories of the end states, | |
| Each leg writes: | |
| - a multistate trajectory (``complex.nc`` and ``solvent.nc``) | |
| - the trajectory's corresponding topology (``alchemical_system.pdb``) | |
| For the default replica exchange sampler (``sampler_method = "repex"``), the trajectory stores the positions of every replica, together with the λ state each replica was in at each iteration. | |
| A ``repex`` trajectory can therefore be read in two ways: at a fixed λ **state**, combining frames from whichever replica occupied that state, or along a single **replica** as it moves between λ states. | |
| With ``"independent"`` sampling, replicas never change state, so both give the same trajectory. | |
| With ``"sams"``, a λ state is not necessarily occupied at every iteration, so reading by state may not be possible. | |
| Only the atoms selected by ``output_indices`` are saved, which by default excludes water. | |
| Both files can be loaded with `openfe_analysis`_ to visualize the simulation, extract the trajectories of the end states, |
I find the block of text difficult to parse as-is. Maybe breaking it up like this would help? It would also be good to link to/from the API sampler_method setting.
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I'm not 100% sure about the way this suggested change written, it reads somewhat oddly.
IAlibay
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Nov 12, 2026
| frames from whichever replica occupied that state, or along a single **replica** as it moves between λ states. | ||
| This applies to the default replica exchange sampler (``sampler_method = "repex"``). | ||
| With ``"independent"`` sampling, replicas never change state, so both give the same trajectory; | ||
| with ``"sams"``, a λ state is not necessarily occupied at every iteration, so reading by state may not be possible. |
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Have we ever checked that SAMS-generated outputs can even be read by openfe-analysis?
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| Each leg writes a multistate trajectory (``complex.nc`` and ``solvent.nc``) with its topology | ||
| (``alchemical_system.pdb``). The trajectory stores the positions of every replica, together with the λ state each | ||
| replica was in at each iteration. A trajectory can therefore be read in two ways: at a fixed λ **state**, combining | ||
| frames from whichever replica occupied that state, or along a single **replica** as it moves between λ states. | ||
| This applies to the default replica exchange sampler (``sampler_method = "repex"``). | ||
| With ``"independent"`` sampling, replicas never change state, so both give the same trajectory; | ||
| with ``"sams"``, a λ state is not necessarily occupied at every iteration, so reading by state may not be possible. | ||
| Only the atoms selected by ``output_indices`` are saved, which by default excludes water. | ||
| Both files can be loaded with `openfe_analysis`_ to visualize the simulation, extract the trajectories of the end states, |
Member
There was a problem hiding this comment.
I'm not 100% sure about the way this suggested change written, it reads somewhat oddly.
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| Each leg writes a multistate trajectory (``complex.nc`` and ``solvent.nc``) with its topology | ||
| (``alchemical_system.pdb``). The trajectory stores the positions of every replica, together with the λ state each | ||
| replica was in at each iteration. A trajectory can therefore be read in two ways: at a fixed λ **state**, combining |
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can therefore be read
Is there something you can link to here to show off how reading works?
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LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution:
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pre-commit.ci autofix.newsentry, or the changes are not user-facing.Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).
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