Preparing multiple simulations for umbrella sampling can be a tedious task. Manually creating conformation-specific folders, specifying initial frames and pulling coordinates for each system variant? It’s time-consuming—and prone to errors.
If you’re using GROMACS and working within SAMSON, there’s an efficient alternative: the Umbrella Sampling batch project generator in the GROMACS Wizard. This tool simplifies the generation of restraint simulations across many conformations by creating ready-to-run simulation folders in bulk. Here’s how it works and why it might simplify your workflow.
Starting from a Trajectory
The most common source of input is a trajectory obtained from another simulation—typically COM pulling. The GROMACS Wizard can automatically detect trajectory files from your project folder. You’ll simply switch to the Umbrella Sampling tab and select your input project. This step will allow you to define your reaction coordinate by selecting two index groups in the system (e.g., atoms or chains whose distance you’re analyzing).
Spacing Strategies for Initial Conformations
Choosing initial conformations is crucial for umbrella sampling. The tool offers two main strategies:
- Number of conformations: Automatically divides the reaction coordinate evenly based on a user-specified number of windows.
- Minimum COM spacing: Selects frames to ensure a minimum center-of-mass distance between them is maintained.
This flexibility gives you control depending on whether your priority is resolution or coverage.
Generate and Organize Automatically
When you finalize your conformational spacing, a single click on Generate project creates a timestamped batch project. Each initial conformation then gets its own folder, fully organized with metadata describing the origin frame from the input trajectory.
The generated frames.ndx file further documents the mapping between trajectory frames and conformations, offering clarity and reproducibility.
Custom Index Groups
In some cases, you might need specific atom groups for pulling or analysis. The wizard lets you add custom index groups before you begin sampling. Doing this early ensures a smoother simulation pipeline later, especially when analyzing PMF results.
When Is This Useful?
If you’re dealing with complex or large systems, or you need dozens of intermediate restraints, the batch setup feature in SAMSON minimizes administrative overhead and lets you focus on analysis—not file management.
It’s especially useful in educational, exploratory, or iterative modeling labs where re-running simulations with new spacing or parameters is routine.
Learn more from the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.