Running an Umbrella Sampling simulation can be time-consuming, especially when it comes to preparing the system correctly. One of the most critical — and often tedious — steps is choosing the right initial conformations. Missteps here can affect the reliability of your entire Potential of Mean Force (PMF) analysis.
The GROMACS Wizard in SAMSON provides a surprisingly flexible solution for this challenge. Whether you already have the results from a GROMACS simulation or you’re working with conformations from a different source, you can quickly generate a structured batch of conformations for Umbrella Sampling. This blog post focuses on the first path: using a GROMACS trajectory to generate a set of distributed initial conformations.
🎯 Step-by-step: From trajectory to batch project
Let’s say you’ve performed a Center of Mass (COM) pulling simulation in GROMACS and now want to use the resulting trajectory frames as the basis for Umbrella Sampling. In SAMSON’s GROMACS Wizard, switch to the Umbrella Sampling tab and choose your project. The wizard will automatically detect the trajectory file.
You’ll then define the reaction coordinate by selecting two index groups — for example, chain A and chain B — used to calculate distances between centers of mass. If needed, you can add custom index groups for later use in analysis or pulling parameters.
📏 Choosing spacing strategies
Here’s where it gets interesting. The GROMACS Wizard offers two intuitive ways to distribute initial conformations along your reaction coordinate:
- Number of conformations: Evenly distribute conformations based on a user-defined quantity, ensuring full reaction coordinate coverage.
- Minimum COM spacing: Choose conformations such that the spatial distance between their COMs meets a defined threshold.
This highly visual interface plots your reaction coordinate and lets you inspect how your chosen conformations are spaced — making the selection process clear and reproducible.
📁 Output: Organized and ready for simulation
Clicking Generate project creates a neatly organized batch project folder. Each sub-folder contains a GROMACS-ready setup for one initial conformation, and a frames.ndx file keeps track of which trajectory frames were used.
This organization simplifies your life for subsequent steps like equilibration and simulation. It minimizes manual file handling and reduces errors from mislabeling or duplicate frames.
🧪 Why this matters
Choosing initial conformations isn’t just about sampling evenly — it’s about striking a balance between computational cost and accurate free energy landscapes. Automating that selection with clear visuals and options integrated into your workflow lowers the barrier to entry for advanced sampling methods.
To learn more, visit the full documentation for Umbrella Sampling in the GROMACS Wizard: https://documentation.samson-connect.net/tutorials/gromacs-wizard/umbrella-sampling/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net.