When launching molecular simulations, especially for systems with flexible conformations, many researchers face a common bottleneck: how to prepare multiple initial states for batch simulations efficiently without duplication of effort. Whether the goal is to explore conformational diversity or sample starting points for ensemble runs, setting up simulations for each state manually can be tedious and error-prone.
Fortunately, the GROMACS Wizard in SAMSON provides a streamlined and reproducible way to set up initial conformations for batch molecular dynamics simulations. Here’s a closer look at how to select and prepare these starting structures using trajectories or sets of conformations.
Why Use Multiple Initial Conformations?
Running simulations from multiple starting points can help:
- Improve sampling of the conformational space
- Capture variability in binding modes or folding landscapes
- Generate statistically significant data from multiple runs
Get Started: Paths or Conformations
In SAMSON, you can use either a conformation path or a collection of distinct conformations as your batch’s initial states. Here’s how each approach works:
✔ Path-based approach
If you’ve manipulated a structure using animations (e.g., docking, undocking, or twisting), SAMSON creates a conformation path. You can also load an existing trajectory from a file.
To extract individual conformations from a path:
- Use the Inspector to browse the path frame-by-frame
- Create conformations manually via Edit > Conformation for frames of interest
- Or auto-generate conformations: right-click the path in the Document View and choose Path > Create conformations from path
✔ Selecting a set of conformations
You may already have several conformations stored as separate models in the SAMSON Document. Simply select them all to define the starting states for the batch project.
Assigning Conformations to Batch Simulations
Once your initial conformations are created or imported, go to the Prepare tab in the GROMACS Wizard and:
- Activate the Batch project mode
- Click on Set conformations or a path after selecting them
- Use the slider to preview and confirm each conformation’s setup
Each selected conformation will be assigned to a numbered subfolder in the batch project. These subfolders operate as fully independent simulations—you can minimize, equilibrate, and run them either locally or in the cloud.
🔍 Batch Project Preview
Use the slider in the Batch preparation box to visually inspect how your periodic box fits around each conformation before moving on to the simulation steps. This is useful to ensure that all starting structures are within reasonable box dimensions.
For a detailed walkthrough of simulation setup after selecting conformations, consult the GROMACS Wizard Step 1: Prepare tutorial.
Final Thoughts
Carefully selecting and preparing multiple initial conformations can make large-scale simulations much more meaningful. SAMSON’s user interface simplifies this process and makes it reproducible. Whether you’re exploring a ligand’s flexibility in binding or seeking a more complete picture of protein dynamics, this capability saves time and improves the quality of your results.
Learn more about batch computations in SAMSON’s GROMACS Wizard
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.