A molecular trajectory can contain far more information than a static structure—but it can also be difficult to know what to do with it next. Should you start another simulation, inspect the path, compare interactions, or send a job to the cloud? Choosing the right next step helps avoid spending time in the wrong part of a workflow.
The useful starting point is simple: identify what you already have. If you have a structure but no path or trajectory, begin with modeling and simulation. If you already have a path or imported trajectory, you can go directly to analysis. That distinction matters because Path Analyzer expects a path in the active document; without one, it is not yet the right place to start.
Choose the next step based on your starting point
- You have a structure and want to explore its motion: start with Modeling and Simulation. This is the entry point for adding simulators, running interactive modeling, and creating conformations or paths.
- You have a path or trajectory and want to examine its evolution: continue to Path Analyzer. It is intended for analyzing paths with observables, plots, and dashboards.
- Your question is about protein–ligand interactions: use Interaction Designer as the analysis destination after simulation.
- Your workflow needs remote computation: consult Cloud computations for remote jobs, monitoring, and result retrieval. Cloud computations require Computing Credits.
A workflow that keeps the question in view
Before launching a simulation, write down what you want to learn. Are you trying to create a path for later analysis, or are you primarily interested in protein–ligand interactions? This small planning step helps you choose a useful destination for the results rather than treating simulation as the finish line.
For a general trajectory-analysis workflow, follow this sequence:
- Start with the structure and use Modeling and Simulation to create conformations or a path.
- Make sure the path is available in the active document before opening Path Analyzer.
- Use Path Analyzer when you want to inspect observables, plots, and dashboards.
- If your focus is protein–ligand interactions, follow the simulation with Interaction Designer instead.
This is not a requirement to use every tool. If you already have an imported trajectory, you can skip the simulation step and go straight to Path Analyzer. If you are working locally and do not need remote jobs, you can skip Cloud computations. A shorter workflow is often the clearer one.
When the analysis does not seem to start
Check the input before changing your workflow. Path Analyzer expects a path in the active document, so confirm that the path or imported trajectory is actually present there. If you only have a starting structure, return to Modeling and Simulation to create a path first. If the task is specifically about protein–ligand interactions, consider whether Interaction Designer is the more relevant destination.
Likewise, remote computation is a choice tied to your task, not a required stage in every simulation. Use the cloud workflow when you need remote jobs, monitoring, or result retrieval, and account for its Computing Credits requirement. For local work, the cloud step can be left out.
Keep the results useful beyond the analysis
Once you have analyzed a path, consider how the result needs to be communicated or reused. The documentation points to Visualize and present for clearer visuals, figures, or movies; Share and collaborate for sharing jobs, documents, or collaboration access; and Automate and extend for scripted analysis and automation.
The main takeaway: let your starting material and scientific question determine the route. Structure first? Simulate. Path already available? Analyze. Interaction question? Choose the interaction-focused route. Remote job needed? Add the cloud workflow. For the complete overview, read the Simulate and analyze documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.