A molecular trajectory can contain a lot of information—and still leave you unsure what to inspect first. You may have a structure ready to simulate, a saved path waiting to be analyzed, or a protein–ligand system whose interactions you want to examine. Choosing the wrong starting point can mean extra setup and a confusing workflow.
A useful way to stay oriented is to begin with one question: What do I have now, and what do I want to learn next? In SAMSON, that question determines whether you should simulate, analyze a path, examine interactions, or run a job remotely.
Start with the data you have
If you have a structure but no path or trajectory: begin with Modeling and Simulation. This is the starting point for adding simulators, running interactive modeling, and creating conformations or paths. The key practical distinction is that analysis of a path comes after you have generated or imported one.
If you already have a path or imported trajectory: go directly to Path Analyzer. It is intended for examining observables, plots, and dashboards. One detail worth checking before you begin: Path Analyzer expects a path in the active document. If the analysis cannot start as expected, confirm that the relevant path is available in the document you are working in.
If your question is about protein–ligand interactions: consider Interaction Designer after simulation. This gives you a workflow focused on analyzing those interactions, rather than treating every analysis question as a general trajectory-inspection task.
A simple workflow that avoids unnecessary steps
- Identify your starting point. Do you have only a structure, a saved path, or an imported trajectory? This tells you whether to start with simulation or analysis.
- Decide what result you need. For an interactive modeling session or a new path, start with Modeling and Simulation. For plots and observables from an existing path, start with Path Analyzer. For protein–ligand interaction analysis, use Interaction Designer.
- Keep the workflow focused. If you want to generate a path and then study its evolution, follow Modeling and Simulation with Path Analyzer. If you want to simulate and then study protein–ligand interactions, follow Modeling and Simulation with Interaction Designer.
- Add remote computing only when the task calls for it. Cloud computations are relevant when you need remote jobs, monitoring, or result retrieval. If you are working locally and do not need remote jobs, you can leave this step out. Cloud computations require Computing Credits.
This order is useful because it separates two different kinds of work: producing molecular motion and interpreting it. A simulator helps create conformations or paths; an analysis tool helps you investigate data you already have. Keeping those stages distinct makes it easier to spot what is missing and to choose the next tool without adding unrelated steps.
Choose the shortest route to your question
- Explore a model interactively: start with Modeling and Simulation.
- Generate a path, then examine it: use Modeling and Simulation followed by Path Analyzer.
- Simulate and inspect protein–ligand interactions: use Modeling and Simulation followed by Interaction Designer.
- Run or retrieve a remote job: consult Cloud computations when cloud execution is part of your workflow.
Once you have results worth communicating, you can continue to Visualize and present. If your next need is sharing documents or access, see Share and collaborate.
For the complete workflow overview and links to each step, read the Simulate and analyze documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.