A molecular simulation can produce a lot of motion—and a lot of data. The difficult part is often deciding what to do next: keep exploring interactively, inspect a saved trajectory, study protein–ligand interactions, or send work to the cloud. Choosing the right next step helps turn a moving structure into an analysis you can actually use.
A helpful way to think about the workflow is as a sequence of questions. First: do you already have a path or trajectory? If not, begin with Modeling and Simulation. If you do, you can often skip straight to analysis.
Start with the kind of result you need
If your immediate goal is to explore a structure interactively or generate conformations and a path, start with the modeling and simulation workflow. Add and run a simulator, then save the conformations or path you want to examine. This gives you a concrete result to carry into the next stage instead of treating simulation and analysis as unrelated tasks.
Before moving on, ask what you want to learn from the motion. Are you interested in observables and plots across a path? Or is your main question about protein–ligand interactions? These are different analysis goals, and the documentation points to different tools for each.
Choose the analysis that matches the question
For a saved path or trajectory, use Path Analyzer to work with observables, plots, and dashboards. One practical detail is easy to overlook: Path Analyzer expects a path in the active document. If you open the analysis tool and do not see the path you expected, check that the relevant path is available in the document you are working with.
If your focus is protein–ligand interactions, continue to Interaction Designer. It is a separate route from general path analysis, so it is useful to decide early whether you are trying to understand how a structure changes over time or to analyze interactions between a protein and a ligand.
Keep remote computing task-specific
Not every workflow needs a cloud job. If you are working locally and do not need remote computing, you can skip the cloud step. If your task does depend on remote jobs, monitoring, or retrieving results, consult Cloud computations. The documentation notes that cloud computations require Computing Credits, so check that requirement when planning the workflow.
A quick decision guide
- No path yet? Start with Modeling and Simulation.
- Have a path and want plots or observables? Continue to Path Analyzer.
- Want to analyze protein–ligand interactions? Use Interaction Designer.
- Need remote execution or result retrieval? Read the cloud workflow guidance; otherwise, leave it out.
This order also helps avoid a common source of frustration: opening an analysis tool before you have the data it needs. First generate or locate the path, then choose the analysis based on the question, and add cloud computing only when the task calls for it. If your next challenge is communicating what you found, continue to Visualize and present. For the complete workflow and links to each step, learn more in the Simulate and analyze documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.