A molecular simulation can produce a lot of motion—and a lot of output. The difficult part is often not simply running a calculation, but knowing what to do next: when to analyze a trajectory, which tool fits the question, and why an analysis tool might have nothing to work with yet.
A useful way to avoid that confusion is to treat the workflow as two stages: create or obtain a path, then analyze it. In SAMSON, the Modeling and Simulation workflow is the starting point for interactive modeling and creating conformations or paths. Once a path or trajectory is available, Path Analyzer is the next stop for observables, plots, and dashboards.
First, identify what you have
Before opening an analysis tool, ask one practical question: do you already have a path or imported trajectory? If not, start with Modeling and Simulation. This keeps the task focused: first prepare the molecular motion you want to study, then inspect its evolution.
If you do already have a path, you can skip the simulation step and go directly to Path Analyzer. One small but important requirement is that Path Analyzer expects a path in the active document. If analysis cannot proceed, check that the path is actually available in the document you are working in before assuming the simulation itself failed.
Match the next step to the question
Not every simulation workflow has the same destination. Use the scientific question to choose the next step:
- Want to create or explore molecular motion interactively? Begin with Modeling and Simulation.
- Want to inspect a saved path or trajectory? Continue to Path Analyzer for observables, plots, and dashboards.
- Want to examine protein–ligand interactions? Use Interaction Designer after the modeling and simulation stage.
- Need a remote job? Consult Cloud computations for remote workflows, monitoring, and result retrieval.
This simple branching step can save time. For example, a user interested in how a structure changes over a trajectory does not need to detour into cloud computing if the work is local. Likewise, someone who only needs to analyze an existing path does not need to repeat the simulation workflow.
A short pre-analysis checklist
- Confirm the input. Is there a path or trajectory to analyze, or do you still need to create one?
- Choose the analysis by purpose. Use Path Analyzer for trajectory observables, plots, and dashboards; use Interaction Designer when the focus is protein–ligand interactions.
- Check the active document. Path Analyzer expects the path there.
- Keep remote work separate from local work. Cloud computations are task-specific, and they require Computing Credits.
- Decide what comes after analysis. Visualize and present results if you need clearer figures or movies; share and collaborate if others need access; explore automation if you want scripted workflows.
Why this order helps
Simulation and analysis answer different questions. Modeling and Simulation helps you generate or explore conformations and paths. Analysis helps you examine what those paths contain. Keeping those roles distinct makes it easier to locate a missing step, choose the right documentation, and avoid opening an analysis workflow before its input is ready.
For a complete route, start with Modeling and Simulation, then continue to Path Analyzer or Interaction Designer, depending on your question. Read the full Simulate and analyze guide to compare the available paths and find the relevant next steps.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.