Extracting a consistent set of initial conformations for Umbrella Sampling is a familiar challenge for molecular modelers. You typically need to split a trajectory, select frames at appropriate intervals along a reaction coordinate, and manually sort everything for batch simulations. This process not only takes time, but it’s also prone to inconsistencies if done manually.
Fortunately, SAMSON’s GROMACS Wizard provides a simple and reproducible way to generate initial conformations for Umbrella Sampling directly from an existing GROMACS trajectory. This feature is especially useful if you’ve already run a pulling simulation (e.g., center-of-mass or COM pulling) and now wish to carry out Umbrella Sampling based on that same trajectory.
From Trajectory to Batch Project
Let’s say you’ve completed a COM pulling simulation and saved the resulting GROMACS trajectory. Instead of manually trimming and extracting frames, open the GROMACS Wizard in SAMSON and switch to the Umbrella Sampling tab. Select your project folder, and the Wizard will automatically detect the appropriate trajectory file. ✅
Define the Reaction Coordinate
Umbrella Sampling relies on pulling along specific reaction coordinates. In this step, you’ll choose two index groups that define this coordinate (for example, two protein chains or a ligand and receptor center-of-mass). You can also define custom index groups earlier in your workflow for more flexibility (see how).
Choose Your Conformations
This might be the most useful part: you have two methods for selecting conformations along your reaction coordinate:
- Number of conformations: evenly distributes the frames based on how many windows you want.
- Minimum COM spacing: lets you define how far apart (in nm) conformations need to be along the reaction coordinate.
The choice depends on your needs—either precision in sampling resolution or ease of automation.
If needed, you can also limit the extraction to specific time intervals by defining the start and end frames. Once your settings are applied, click Generate project. The Wizard outputs a clean and timestamped _umbrella batch project folder. Each subfolder contains a project for a given initial conformation, and a frames.ndx file lists the selected frames.
Why This Matters
This workflow significantly accelerates and standardizes the preparation of Umbrella Sampling simulations. Automatically parsing your trajectory, selecting consistent initial conformations, and packaging them as a batch project saves time—and reduces errors in setup.
If you’ve ever spent hours splitting trajectory files and tracking frame indexes, this approach simplifies your work while remaining flexible enough for more advanced users who need custom index groups or specific spacing criteria.
To learn more, visit the Umbrella Sampling documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.