A molecular trajectory can contain a lot of information—and still leave you unsure what to do next. You may have watched a structure move during a simulation, but now you need to decide whether to analyze the path, inspect protein–ligand interactions, or send a calculation to the cloud. Choosing the right next step helps turn motion into results you can interpret and communicate.
A useful way to think about the workflow is as two separate questions: How will I generate or obtain the molecular motion? And what do I want to learn from it? In SAMSON, the documentation connects these questions through modeling and simulation, followed by the analysis tool that fits your goal.
Start with what you have
If you are starting from a molecular structure and want to run interactive modeling or create conformations or paths, begin with Modeling and Simulation. This is the foundation for adding simulators and generating the material you may want to study afterward.
If you already have a path or an imported trajectory, you may not need to revisit the simulation step. You can go directly to Path Analyzer when your goal is to inspect observables, plots, or dashboards. One practical detail matters: Path Analyzer expects a path in the active document. If the analysis option does not match what you currently have open, first check that the path is available in the active document.
Choose analysis by the question
Before opening an analysis tool, write down the question you want the trajectory to help answer. This small step can keep you from exploring outputs without a clear purpose.
- Interested in changes along a path? Use Path Analyzer to work with observables, plots, and dashboards.
- Interested in protein–ligand interactions? Continue from simulation to Interaction Designer.
- Still deciding what to run? Start with Modeling and Simulation, then choose the analysis path that fits the question you want to investigate.
These are different analysis goals, not interchangeable steps. Choosing between them early makes the workflow easier to follow and helps you spend time on the results relevant to your project.
Keep remote computing an intentional choice
Not every workflow needs a remote job. If your work is local, the cloud step can be skipped. If you do need remote jobs, monitoring, or result retrieval, consult Cloud computations. The documentation notes that Cloud computations requires Computing Credits, so it is worth checking this requirement before planning a cloud-based workflow.
A simple route through the work
- Identify whether you are beginning with a structure or already have a path or trajectory.
- If you need to generate motion, read Modeling and Simulation.
- Choose the analysis tool based on your question: Path Analyzer for path observables and plots, or Interaction Designer for protein–ligand interactions.
- Use Cloud computations only if your task calls for remote jobs, monitoring, or retrieving results.
- After analyzing the results, consider how you will present or share them. The documentation points to Visualize and present and Share and collaborate as next steps.
The central habit is simple: match the tool to the question, and confirm that the data needed for that step is available. A path is useful when you want to analyze change over time; interaction analysis addresses a different kind of question; remote computing is an option when the workflow requires it.
For the full workflow and links to each guide, see Simulate and analyze.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.