A molecular simulation can produce a lot of motion—and a lot of saved data. But when the run is over, a common question remains: what should you examine next? Without a clear route from simulation to analysis, it is easy to spend time looking at structures without knowing which tool or workflow fits the question.
A useful way to think about the process is as a sequence: create or obtain a path, analyze it, then choose any follow-up work based on what you need to learn. In SAMSON, the starting point depends on whether you already have a path or trajectory.
Start with the data you have
If you are beginning with a molecular structure and want to run interactive modeling, start with Modeling and Simulation. This is where the documented workflow begins for adding simulators, running interactive modeling, and creating conformations or paths.
If you already have a path or an imported trajectory, you can skip that preparation and go directly to Path Analyzer. The important prerequisite is that a path must be available in the active document. Checking this first can save a detour: if Path Analyzer has nothing to work with, return to the simulation or import step before troubleshooting the analysis itself.
Match the analysis to the question
Path Analyzer is the documented destination when you want to examine observables, plots, and dashboards from a path or trajectory. Before opening it, write down the question you want the analysis to help answer. Are you trying to compare how a structure changes over time, or do you need a visual summary of a trajectory? A specific question makes it easier to decide what to inspect and what results are relevant.
If your focus is protein–ligand interactions rather than general trajectory analysis, the recommended route is to start with Modeling and Simulation and then continue to Interaction Designer. This distinction helps avoid treating every analysis task as the same problem: use Path Analyzer for path-based observables and plots, and Interaction Designer when the goal is interaction analysis.
Choose local or cloud work deliberately
Not every workflow needs a remote job. If you are working locally and do not need remote computation, the cloud section can be skipped. If your task does depend on a remote job, consult Cloud computations for the workflow around running jobs, monitoring them, and retrieving results. The documentation notes that Cloud computations requires Computing Credits, so factor that into your plan before choosing this route.
A practical route through the workflow
- Starting from a structure: use Modeling and Simulation to run interactive modeling and create a path or conformations.
- Ready to inspect a path: confirm the path is in the active document, then use Path Analyzer for observables, plots, and dashboards.
- Studying protein–ligand interactions: follow the simulation step with Interaction Designer.
- Needing remote execution: consult the cloud workflow and account for its Computing Credits requirement.
Once the simulation and analysis are complete, the next step may be communication rather than more computation. The documentation points to Visualize and present for clearer visuals, figures, or movies, and to Share and collaborate when you need to share documents, jobs, or collaboration access.
The short version: begin with the question, check whether you already have a path, and choose the analysis tool that matches the task. For the complete workflow and links to each step, read the Simulate and analyze guide.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.