One of the more time-consuming steps when performing umbrella sampling simulations is generating a consistent and well-distributed set of initial conformations along a reaction coordinate. If you’ve done this manually, you probably know the frustration of extracting frames from a trajectory, computing distances, and ensuring uniform sampling.
Fortunately, the GROMACS Wizard in SAMSON provides a visual, integrated solution for this exact challenge. In this post, we’ll explore the workflow to generate a batch project for umbrella sampling using an existing GROMACS trajectory — a task that often plagues molecular modelers with tedious scripting and uncertainty.
Start with a Trajectory
Let’s assume you already have a GROMACS trajectory from a simulation — perhaps from center-of-mass (COM) pulling. In SAMSON, switching to the Umbrella Sampling tab of the GROMACS Wizard lets you directly load this project. The tool automatically identifies the trajectory file in the project folder.
Pick the Reaction Coordinate
The next step is to define the reaction coordinate — usually the distance between two groups (e.g., protein chains, atoms, or residues). You select two index groups from your system, like chain A and chain B.
You also have the option to add your own index groups, which can later be used in pulling parameters or analysis. This ensures flexibility no matter how your system is organized. A real timesaver if you’ve had to hack together index groups manually.
Control the Sampling Distribution
One great feature is the ability to see the reaction coordinate over time and choose how to space frames along it. You can choose:
- Number of conformations, evenly spaced along the coordinate, or
- Minimum COM spacing, ensuring a physical spacing between samples.
You can also restrict the sampling to a specific region in your trajectory using explicit start and end frames. This lets you avoid unstable regions or equilibration artifacts.
Batch Project Output
Once you’re happy with the spacing, click Generate project. The tool creates a batch project folder with subdirectories for each conformation. Everything is organized and timestamped for traceability. It even includes a frames.ndx file, documenting which frames were selected — transparency built-in.
This automated approach eliminates the guesswork and scripting usually associated with preparing umbrella sampling trajectories. It saves both time and effort while helping ensure consistency across sampling windows.
To learn more and explore the complete workflow, including equilibration and PMF analysis, visit the full documentation: GROMACS Wizard – Umbrella Sampling.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.