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Simulate and analyze#

Use this topic when you want SAMSON to do more than static editing and viewing. It covers interactive simulation, path and trajectory analysis, and cloud workflows for jobs that run beyond the local application. Follow the full sequence if you are starting from a structure, or jump straight to analysis if you already have a path.

Who this topic is for#

  • Users launching interactive simulations
  • Users analyzing saved paths or trajectories
  • Users running remote jobs
  • Users comparing structure evolution over time

What you will be able to do afterward#

  • Add and run simulators
  • Save conformations and paths
  • Analyze trajectories with Path Analyzer
  • Analyze protein-ligand interactions with Interaction Designer
  • Monitor and retrieve cloud job results
  1. Modeling and Simulation - Start here to add simulators, run interactive modeling, and create conformations or paths. Foundational.
  2. Path Analyzer - Continue here once you have a path or trajectory and want observables, plots, and dashboards. Foundational for analysis.
  3. Interaction Designer - Continue here if you want to analyze protein-ligand interactions. Foundational for analysis.
  4. Cloud computations - Read this when your workflow depends on remote jobs, monitoring, or result retrieval. Optional / task-specific.

Read this first#

Start with Modeling and Simulation. If you already have a path or imported trajectory and only need analysis, you can jump directly to Path Analyzer.

You can skip this for now if...#

  • You do not yet have a path or trajectory, in which case you can skip Path Analyzer
  • You are working locally and do not need remote jobs, in which case you can skip Cloud computations

Suggested paths#

Where to go next#

  • Visualize and present - Continue here when you want to communicate results through clearer visuals, figures, or movies.
  • Share and collaborate - Go here when you need to share jobs, documents, or collaboration access.
  • Automate and extend - Continue here when you want scripted analysis, automation, or extension-based workflows.

Notes#

Cloud computations requires Computing Credits, and Path Analyzer expects a path in the active document.