A molecular trajectory can contain a great deal of information—and still leave you wondering what changed, when it changed, or which interactions matter. The key is to treat simulation and analysis as connected steps, while recognizing that they are separate tasks: first create or obtain a path, then choose the analysis that answers your question.
Start with the question, not the plot
Before running a simulation, decide what you hope to learn. Are you exploring how a structure changes during interactive modeling? Do you already have a saved path or imported trajectory and want to examine observables over time? Or is your main question about protein–ligand interactions? These goals point to different parts of the SAMSON workflow.
- To create conformations or paths: begin with Modeling and Simulation. This is the starting point for adding simulators, running interactive modeling, and generating paths.
- To inspect an existing path or trajectory: use Path Analyzer to work with observables, plots, and dashboards.
- To focus on protein–ligand interactions: follow the relevant analysis workflow with Interaction Designer.
The handoff that is easy to miss
Analysis depends on having something to analyze. Path Analyzer expects a path in the active document. If you open the analysis step before creating or bringing in a path, you may find yourself stuck—not because the analysis question is wrong, but because its input is missing.
A simple workflow check can prevent that detour:
- Identify whether you already have a path or trajectory.
- If not, start with Modeling and Simulation and create conformations or a path for your workflow.
- Make sure the path is available in the active document before proceeding to Path Analyzer.
- Choose the analysis route that matches your question: general path observables, or protein–ligand interactions.
This sequence also helps separate two different kinds of uncertainty. If you do not yet have a trajectory, the next task is simulation or modeling. If you do have one, the next task is deciding what to measure and how to inspect its evolution.
Keep the workflow proportional to the task
Not every molecular modeling session needs every tool. For interactive modeling, you can start with the simulation material and stop there. If you already have a path, you can go directly to Path Analyzer instead of repeating the simulation steps. If you are working locally, cloud computations are not required.
For longer or remote work, SAMSON’s cloud workflow can be used to run jobs, monitor them, and retrieve results. Treat it as a task-specific branch rather than a mandatory part of trajectory analysis: cloud computations require Computing Credits, while local workflows do not need that step.
Make the result easier to communicate
Analysis is most useful when it connects back to the original question. Keep track of what input you analyzed, which route you used, and what the plots or interaction analysis are intended to clarify. If the next challenge is explaining the result to someone else, continue to Visualize and present for clearer visuals, figures, or movies. For shared jobs or collaboration access, see Share and collaborate.
The central troubleshooting question is simple: Do I have a path in the active document yet? Answering it first can save time and make the route through simulation, trajectory analysis, interaction analysis, and optional cloud work much clearer.
Learn more in the Simulate and analyze documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.