Setting up an umbrella sampling simulation can be a tedious process, especially when trying to decide which snapshots to use as initial conformations. Molecular modelers often find themselves manually selecting frames from trajectories or trying to estimate proper spacing between them—a task that’s not just time-consuming but also prone to inconsistencies.
The GROMACS Wizard, available in the SAMSON platform, offers a more guided and visual approach to solve this pain point. In this post, we explore how SAMSON helps users efficiently choose initial conformations using a reaction coordinate profile—without doing it manually or relying on external scripts.
A Visual Way to Select Initial States
One of the most common pain points when setting up umbrella sampling is having to manually scan through large MD trajectories to extract representative configurations. GROMACS Wizard eliminates this by generating a distance vs time plot of the chosen reaction coordinate, where it suggests initial conformations using vertical and horizontal dashed lines.
Choose by Number or Spacing
Once your reaction coordinate is defined (e.g., distance between two chains), the next step is to decide how to space out your initial snapshots. Here, you have two straightforward options:
- Number of conformations: Set a total number, and GROMACS Wizard ensures they’re evenly distributed along the coordinate.
- Minimum COM spacing: Specify a minimum center-of-mass (COM) distance between frames. The wizard selects frames accordingly to ensure no two selected conformations are closer than the specified threshold.
What You Get
After specifying the spacing criteria, clicking on Generate project creates a batch folder with individual projects for each selected conformation, as well as a frames.ndx file that records which trajectory frames were picked. It’s all neatly organized, eliminating the need for any manual indexing or scripting.
Small Tweaks, Big Time Savings
This guided workflow is more than just a convenience—it helps produce consistent and reproducible simulations. By letting the tool guide you based on clear visual criteria, you can spend less time on setup and more time analyzing results.
To dive deeper into setting up umbrella sampling and explore the full tutorial, including the subsequent steps like NPT equilibration and PMF analysis, visit the official documentation: 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 at https://www.samson-connect.net.