A molecular simulation can produce a path or trajectory full of structural changes—but the result is not automatically an answer. The common challenge is knowing what to do next: how to move from running a simulation to examining the motion, understanding interactions, or retrieving results from a remote job.
A useful way to avoid getting lost is to treat simulation and analysis as separate stages. First, create or obtain the data you want to study. Then choose the analysis tool that matches your question. In SAMSON, this makes it easier to focus on the next scientific step rather than trying to follow every workflow at once.
Start with the question
Before opening an analysis tool, decide what you need to learn. Are you still building and running a model? Do you already have a path and want to inspect observables or plots? Or are you specifically interested in protein–ligand interactions? These questions point to different places in the workflow.
- You need to run interactive modeling: begin with Modeling and Simulation. This is the starting point for adding simulators, running interactive modeling, and creating conformations or paths.
- You already have a path or trajectory: go to Path Analyzer to work with observables, plots, and dashboards.
- Your question is about protein–ligand interactions: use Interaction Designer as the analysis destination.
- Your computation runs remotely: consult Cloud computations for the cloud workflow, including monitoring and result retrieval.
Keep the handoff between stages clear
If you are starting from a structure, the basic sequence is straightforward: use Modeling and Simulation to generate conformations or a path, then move to the analysis that addresses your question. For path-focused analysis, the sequence is Modeling and Simulation → Path Analyzer. For interaction-focused analysis, it is Modeling and Simulation → Interaction Designer.
This distinction matters because analysis depends on having the right input. Path Analyzer expects a path in the active document. If you are ready to analyze but the tool has nothing to work with, check first whether the relevant path is available in the document you are using. If you have not generated or imported a path yet, return to the modeling stage rather than treating the missing analysis result as a problem with the analyzer.
Choose the shortest route that fits
Not every project needs every part of the workflow. If you already have a trajectory, you can skip the simulation introduction and go straight to Path Analyzer. If your work is entirely local, you can leave cloud computations aside. Conversely, if a job is remote, the cloud page is the relevant place to learn about monitoring and retrieving its results.
This gives you a simple checkpoint before you begin: What do I have, and what do I want to find out? If you have a structure but no path, start with simulation. If you have a path, choose an analysis tool. If the job is remote, include the cloud workflow. Avoiding unnecessary steps can make a complex molecular modeling task easier to navigate.
After the analysis
Analysis is often not the final step. If you need to communicate what you found, continue to Visualize and present for clearer visuals, figures, or movies. If the next need is collaboration, see Share and collaborate. For scripted analysis or automation, continue to Automate and extend.
The key is to connect each stage to a concrete need: create motion, inspect a path, study interactions, or manage a remote job. For the complete workflow and links to each topic, see the SAMSON guide to simulating and analyzing.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.