A molecular trajectory can contain a lot of information—and still leave you unsure what to look at first. You may have a structure on screen, a simulation in progress, or a saved path, but those are different stages of a workflow. Choosing the right next step helps avoid a common frustration: opening an analysis tool before there is anything for it to analyze.
In SAMSON, the useful starting question is simple: Do you already have a path or trajectory in the active document? Your answer determines where to begin.
If you are starting from a structure
Begin with Modeling and Simulation. This is the foundational part of the workflow for adding simulators, running interactive modeling, and creating conformations or paths. Think of it as the step that produces the changing structural data you will later want to inspect.
Before moving on, be clear about what you have created or saved. A static structure is not the same as a path or trajectory: the latter gives you structural evolution to examine. If your goal is to understand changes over time, generating or importing that evolving data is a necessary first step.
If you already have a path
Go to Path Analyzer. It is intended for analyzing paths and trajectories, including observables, plots, and dashboards. One important practical detail: Path Analyzer expects a path in the active document. If the analysis you want is not available, first check whether the relevant path is actually present in the document you are working in.
A productive way to approach trajectory analysis is to connect each question to something you can inspect. For example, ask what you want to compare across the path, then use the available observables and plots to help examine that evolution. A dashboard can help bring analysis views together. The aim is not to produce more plots for their own sake; it is to make the structural changes relevant to your question easier to see and discuss.
When the question is about binding interactions
Not every analysis question is a general trajectory question. If you specifically want to analyze protein–ligand interactions, the documentation points to Interaction Designer. A useful workflow is therefore to simulate or generate a path first, then choose the analysis tool that matches what you want to learn: Path Analyzer for trajectory analysis, or Interaction Designer for protein–ligand interactions.
When to use cloud computations
Remote jobs are a separate workflow choice, not a required step for every simulation. If your work depends on running jobs remotely, monitoring them, or retrieving their results, consult Cloud computations. If you are working locally and do not need remote jobs, you can leave this part out. The documentation notes that Cloud computations requires Computing Credits, so it is worth checking that requirement before planning a cloud-based workflow.
A quick decision guide
- Starting with a structure? Begin with Modeling and Simulation.
- Have a path or trajectory in the active document? Continue with Path Analyzer.
- Focused on protein–ligand interactions? Consider Interaction Designer.
- Need remote jobs or result retrieval? Read the Cloud computations guide and account for Computing Credits.
This order keeps the workflow grounded in what you already have: create or obtain evolving structural data, then select an analysis path based on the scientific question. For the complete overview and links to each stage, see the Simulate and analyze documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.