A molecular simulation can produce a lot of motion—and a lot of saved data. The difficult part often comes next: deciding what to do with a structure, path, or trajectory, and finding the right analysis step without losing track of what you need first.
A useful way to approach the workflow is to begin with one question: Do I already have a path or trajectory to analyze? Your answer determines where to start.
Starting with a structure
If you are beginning from a molecular structure and want to explore how it changes, start with Modeling and Simulation. This is the foundational step for adding simulators, running interactive modeling, and creating conformations or paths.
Think of this stage as producing the material for a later question. For example, you might first need to generate a path before you can inspect observables or plots along it. Keeping those stages distinct can make a workflow easier to plan: first create the motion or path, then decide how to examine it.
Already have a path? Go straight to analysis
If you already have a path or an imported trajectory, you do not need to repeat the simulation step just to begin analysis. Go directly to Path Analyzer. It is intended for analyzing paths and trajectories with observables, plots, and dashboards.
One practical detail is easy to miss: Path Analyzer expects a path in the active document. Before troubleshooting the analysis itself, check that the relevant path is available in the document you are working in. This small check can help distinguish a missing input from a problem with the analysis you intended to perform.
Choose the analysis based on the question
Not every simulation workflow is aimed at the same kind of result. If you want to inspect a path or trajectory, Path Analyzer is the relevant destination. If your question is specifically about protein–ligand interactions, the recommended route is to start with Modeling and Simulation and then continue to Interaction Designer.
This distinction is useful when planning work with collaborators, too: describing whether the goal is trajectory analysis or interaction analysis makes it clearer which part of the workflow should come next.
When does cloud computing belong in the workflow?
Cloud computations are optional and task-specific, rather than a required step for every simulation. Consider the Cloud computations guide when your workflow depends on remote jobs, monitoring them, or retrieving their results. If you are working locally and do not need remote jobs, you can skip this part.
Cloud computations require Computing Credits, so it is worth checking that requirement before organizing a workflow around a remote job. For a local task, there is no need to add a cloud step simply because it appears in the broader simulation-and-analysis sequence.
A quick route map
- Interactive modeling: begin with Modeling and Simulation.
- Create a path, then analyze it: Modeling and Simulation → Path Analyzer.
- Simulate, then examine protein–ligand interactions: Modeling and Simulation → Interaction Designer.
- Run or manage remote work: consult Cloud computations when remote jobs are part of the task.
The simplest way to avoid an unnecessary detour is to identify your starting point and desired result before choosing a guide. A structure without a path usually calls for modeling and simulation first. An existing path can take you directly to analysis. A protein–ligand question points toward Interaction Designer, while remote execution brings cloud workflows into scope.
For the complete workflow overview and links to each step, see the Simulate and analyze documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.