A molecular simulation can produce a lot of motion—and a lot of uncertainty. You may have a saved path or trajectory, but still need to decide what to inspect, which tool to use, and whether you need to run another simulation at all. Separating those decisions makes the workflow easier to manage.
The key distinction is between generating a path and analyzing one. Modeling and Simulation is the starting point when you need to add a simulator, run interactive modeling, or create conformations or paths. Path Analyzer is the next stop when a path or trajectory already exists and you want to examine observables, plots, and dashboards. If your immediate question is about protein–ligand interactions, Interaction Designer is the more relevant analysis route.
First, identify what you have
Before opening an analysis tool, ask one simple question: is there already a path or trajectory to examine? If not, begin with Modeling and Simulation. That page is the foundation for adding simulators, running interactive modeling, and creating conformations or paths.
If you already have a path or imported trajectory, you can skip the simulation step and go directly to Path Analyzer. One detail matters: Path Analyzer expects a path in the active document. If the analysis does not seem to match the data you intend to inspect, first check that the relevant path is present in the document you are working with.
Choose the analysis that matches the question
- Want to inspect a trajectory? Use Path Analyzer to work with observables, plots, and dashboards.
- Want to examine protein–ligand interactions? Follow the simulation workflow, then use Interaction Designer for that interaction-focused analysis.
- Need to run work remotely? Consult Cloud computations for remote jobs, monitoring, and retrieving results. Cloud computations require Computing Credits.
This small decision tree helps avoid a common source of wasted effort: trying to answer an analysis question before a suitable path exists, or launching a new simulation when the path you need is already available.
A dependable sequence
- Start with the scientific question. Decide whether you need to create molecular motion, inspect a path, study protein–ligand interactions, or run a remote job.
- Create a path only when needed. If you are starting from a structure and need to simulate, begin with Modeling and Simulation. Save the conformations or paths required for the later analysis.
- Move to the matching analysis page. Use Path Analyzer for path-based observables, plots, and dashboards; use Interaction Designer when the focus is protein–ligand interactions.
- Check the document context. For Path Analyzer, make sure the path is in the active document before beginning.
- Add cloud work only if the task calls for it. If your workflow depends on remote computation, include the cloud job’s monitoring and result-retrieval steps, and account for the Computing Credits requirement.
Keeping these stages separate also makes results easier to revisit: simulation creates the material for analysis, while analysis helps you inspect what that material contains. If you already have a path, there is no need to read every section in sequence—go straight to the relevant analysis guide. If you are working locally and do not need remote jobs, the cloud section can wait.
After analyzing a path, consider how you will communicate what you found. The guides for Visualize and present, Share and collaborate, and Automate and extend cover useful next steps for presenting results, sharing work, or building scripted workflows.
For the full workflow overview, see Simulate and analyze.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.