For molecular modelers performing umbrella sampling, generating initial conformations can often feel like a tedious and error-prone process. Whether you’re dealing with long trajectories or a set of predefined conformations, deciding where to extract your snapshots isn’t always straightforward. The GROMACS Wizard in SAMSON offers a streamlined solution that can help you efficiently prepare for umbrella sampling by guiding you through this essential step.
This post explores how to use the Umbrella Sampling tab in the GROMACS Wizard to generate a batch project with initial conformations derived from a GROMACS trajectory. If your goal is to avoid jumping between scripts and visualizers and instead extract conformations in a few clicks, you’ll find this approach useful.
Start With a Trajectory
To begin, switch to the Umbrella Sampling tab in the GROMACS Wizard and choose your input project. SAMSON will automatically detect the trajectory file from the selected project.
Define the Reaction Coordinate
Next, you specify the reaction coordinate by selecting two index groups. This defines what distance or interaction you’re analyzing in the umbrella sampling. You can also add custom index groups if needed, for example if your system involves atoms from different chains or ligands.
Visualize and Pick Conformations
Once the reaction coordinate is defined, SAMSON displays a plot of distance versus time from your trajectory. Vertical and horizontal dashed lines help visualize suggested initial conformations based on spacing options that you specify.
You have two main options to select conformations:
- Number of conformations – SAMSON evenly distributes conformations across the reaction coordinate.
- Minimum COM (center of mass) spacing – Useful when you want to avoid redundant snapshots and ensure physical separation between conformations.
Below is the interface where you select based on the number of conformations:
And here is the COM spacing view:
You can also define the range of trajectory frames you want to use, which adds further control when, for example, your system stabilizes only after a few nanoseconds.
Generate the Batch Project
After selecting your conformations, click Generate project. SAMSON will create a new batch project folder with timestamp and _umbrella suffix. Each subfolder corresponds to one initial conformation and contains all necessary files to continue with the umbrella sampling simulation. A file named frames.ndx keeps track of which trajectory frames were chosen.
Why This Matters
Manually selecting initial conformations—especially from long trajectories—can take hours. With this feature, you can visually check spacing, control precision, and generate analysis-ready folders in just a few steps. If you’re conducting free energy calculations or exploring reaction mechanisms, this step saves not just time, but also ensures consistency across your simulations.
This functionality is integrated as part of the GROMACS Wizard in SAMSON, and helps reduce the chances of errors while increasing reproducibility.
Learn more about the complete workflow for umbrella sampling in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.