A molecular simulation can produce a sequence of changing structures, but watching that sequence is not the same as understanding it. When you need to compare conformations, inspect how a system evolves, or communicate what happened, the useful question is not only “What does the trajectory look like?” It is also “What can I measure or compare along the way?”
In SAMSON, a practical workflow is to start with modeling and simulation, save a path or trajectory, and then analyze it with the tool suited to your question. This simple order helps avoid a common frustration: opening an analysis tool before the data it needs is available.
Start with the data you actually have
If you are beginning with a molecular structure and want to create conformations or a path, begin with Modeling and Simulation. That is where you can add simulators, run interactive modeling, and create the data that later analysis can examine.
If you already have a path or an imported trajectory, you may be able to skip the simulation step and go directly to Path Analyzer. The important prerequisite is that a path is present in the active document. If Path Analyzer does not have a path to work with, check the document and the data you have opened before looking for a more complicated explanation.
Choose analysis according to the question
Different questions call for different follow-up steps. Use Path Analyzer when you want to explore a path or trajectory through observables, plots, and dashboards. These views can help turn a long sequence of structures into information you can inspect and compare, rather than relying only on visual playback.
If your main question concerns protein–ligand interactions, the relevant next step is Interaction Designer. The distinction is useful: first decide whether you need to understand the broader evolution of a path or focus specifically on interactions between a protein and a ligand. That decision gives your analysis a clearer purpose and helps you select the appropriate documentation.
A workflow that keeps the steps connected
- Prepare or open your molecular system. If you still need to generate conformations or a path, start with Modeling and Simulation.
- Run the simulation and save the result you intend to inspect. Keep track of whether you are working with a path or a trajectory so you can choose the appropriate analysis route.
- Confirm the path is in the active document. Path Analyzer expects a path there; this is a useful check before beginning analysis.
- Match the analysis tool to the question. Use Path Analyzer for observables, plots, and dashboards, or Interaction Designer when focusing on protein–ligand interactions.
- Decide whether the work needs to run remotely. For workflows involving remote jobs, monitoring, or retrieval of results, consult Cloud computations. Cloud computations require Computing Credits. If you are working locally and do not need remote jobs, you can leave this step out.
Make the result easier to explain
Analysis is most useful when it answers a question someone else can understand. Before presenting a plot or a trajectory, state what you wanted to investigate, what path or trajectory you examined, and which analysis route you used. If the result needs a clearer visual explanation, continue to Visualize and present. If you need scripting or an extension-based workflow, see Automate and extend.
The key habit is to treat simulation and analysis as connected stages, while still letting your question determine where you begin. Starting from a structure? Generate a path first. Already have a path? Go straight to analysis. Need remote execution? Add the cloud workflow only when it is relevant.
For the full workflow and links to each step, see the SAMSON guide to simulating and analyzing.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.