A molecular structure can look complete on screen and still leave the important question unanswered: what happens as it changes? For modelers, the challenge is often not simply starting a simulation. It is knowing what to do next—how to create a path, where to inspect it, and which analysis tool fits the question.
A useful way to avoid a dead end is to treat simulation and analysis as a sequence. First, generate or obtain a path or trajectory. Then choose the analysis that matches what you want to learn. In SAMSON, this means starting with Modeling and Simulation for interactive modeling and creating conformations or paths, then moving to an analysis tool when you have the data it needs.
Start with the object you actually have
If you have a structure but no path yet, begin with Modeling and Simulation. This is the foundational stop for adding simulators, running interactive modeling, and creating conformations or paths. It helps establish the material that later analysis depends on.
If you already have a path or imported trajectory, you can skip the simulation step and go directly to Path Analyzer. The key prerequisite is that a path must be available in the active document. If Path Analyzer does not have the path it expects, check that you are working in the document containing it before looking for analysis results.
This simple check saves time: distinguish between “I need to produce molecular motion” and “I have molecular motion and need to inspect it.” The tools are related, but they solve different stages of the task.
Choose analysis by scientific question
For a path or trajectory, Path Analyzer is the next stop when you want to examine observables, plots, and dashboards. A practical way to use it is to begin with the question you need the analysis to answer, then use the available observables and plots to inspect how the path evolves. Keeping the question in view makes it easier to turn a collection of frames into a focused analysis.
If your question is specifically about protein–ligand interactions, the relevant route is Interaction Designer. The distinction matters: a general trajectory analysis and an analysis centered on protein–ligand interactions are not interchangeable goals. Picking the route before you begin can make the workflow clearer.
Keep remote work optional
Not every project needs cloud computing. If your workflow is local, you can skip the cloud section. If you do need remote jobs, monitoring, or result retrieval, consult Cloud computations. Plan for the stated requirement: Cloud computations requires Computing Credits. Keeping this separate from the local simulation-and-analysis route helps you avoid treating cloud setup as a mandatory step.
A quick workflow checklist
- Starting from a structure? Use Modeling and Simulation to run interactive modeling and create conformations or paths.
- Already have a path or trajectory? Make sure it is in the active document, then use Path Analyzer for observables, plots, and dashboards.
- Studying protein–ligand interactions? Continue to Interaction Designer.
- Need remote execution? Use Cloud computations for remote jobs and their monitoring or retrieval, and account for Computing Credits.
The main lesson is to let your current input and scientific question determine the next tool. A structure points toward simulation; a path points toward trajectory analysis; a protein–ligand question points toward interaction analysis; and remote execution is a task-specific branch rather than a requirement for everyone.
For the complete workflow overview and links to the related guides, learn more in the SAMSON documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.