A simulation can produce a lot of motion—and a familiar challenge for molecular modelers is deciding what to do with it next. Should you keep adjusting the model, inspect a trajectory, study protein–ligand interactions, or send a job to the cloud? Choosing the right next step helps turn a moving structure into an analysis you can actually use.
SAMSON’s simulation and analysis workflow offers a straightforward way to make that choice. The key question is not simply “What tool should I open?” but “What do I have, and what do I want to learn from it?”
Start with what you have
If you are starting with a structure and want to run interactive modeling, begin with Modeling and Simulation. This is the foundational step for adding and running simulators and creating conformations or paths.
If you already have a path or imported trajectory and your goal is to examine its evolution, you can skip ahead to Path Analyzer. It is intended for analyzing paths with observables, plots, and dashboards. One important prerequisite: the Path Analyzer expects a path in the active document. Before beginning, check that the path you want to study is available in the document you are working in.
This simple distinction can save time. If you do not yet have a path or trajectory, analysis is not the first step; start by modeling and generating one. If you already have one, there is no need to repeat the simulation workflow just to reach analysis.
Match the next step to the question
- Want to explore or create molecular motion? Start with Modeling and Simulation.
- Want to examine a path or trajectory? Continue to Path Analyzer.
- Want to focus on protein–ligand interactions? Use Interaction Designer as the analysis destination after modeling and simulation.
- Need a remote job, monitoring, or result retrieval? Consult Cloud computations.
These are related routes, not a requirement to use every tool in sequence. For example, a common path is modeling and simulation followed by Path Analyzer. If the question is specifically about protein–ligand interactions, the route can instead lead to Interaction Designer. Cloud computations are task-specific: if your work is local and does not require remote jobs, you can leave that section aside.
A practical pre-analysis check
Before opening an analysis tool, take a moment to clarify three things:
- Your starting point: Are you beginning with a structure, or do you already have a path or trajectory?
- Your analysis goal: Do you want observables and plots for a path, or do you want to analyze protein–ligand interactions?
- Your computing setup: Does the task need a remote job, or can it stay local?
Then follow only the branch that fits. Starting from a structure? Begin with Modeling and Simulation. Have a path ready? Go to Path Analyzer, making sure the path is in the active document. Investigating protein–ligand interactions? Choose Interaction Designer. Need remote execution or retrieval? Read the cloud workflow first; cloud computations require Computing Credits.
Thinking in terms of starting point, question, and computing setup makes the workflow easier to navigate—and helps prevent a common source of frustration: looking for an analysis result before the required path is available, or spending time on remote-job instructions for a local task.
After the analysis
Once you have results, the next useful step may be communicating them, sharing work, or automating part of the workflow. The documentation points to Visualize and present for clearer visuals, figures, or movies; Share and collaborate for sharing jobs, documents, or access; and Automate and extend for scripted analysis and extension-based workflows.
For the complete overview of simulation, analysis, and cloud workflows, see the SAMSON Simulate and analyze guide.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.