When setting up umbrella sampling simulations, molecular modelers often ask a critical question: how should I choose initial conformations along my reaction coordinate? Selecting poorly spaced conformations or skipping key intermediates may lead to biased potential of mean force (PMF) profiles and inaccurate free energy calculations.
The GROMACS Wizard in SAMSON provides an interface to generate initial conformations from a trajectory in a pain-free way. In this post, we’ll focus on the process of extracting evenly spaced conformations from a GROMACS trajectory—an essential step toward accurate umbrella sampling.
Step-by-step: Extracting Initial Conformations
Once you’ve run a center-of-mass (COM) pulling simulation, like the one covered in this tutorial, you’re ready to select frames for umbrella sampling.
In the GROMACS Wizard, switch to the Umbrella Sampling tab. Begin by selecting the relevant input project. The wizard will fetch the associated trajectory from the project folder.
Next, define the reaction coordinate by selecting two index groups—typically, groups representing molecular domains such as protein chains or atoms of interest.
Tip
If needed, you can add your own index groups in the Preparation step for more flexibility.
The wizard will then display a distance vs. time plot for the reaction coordinate. Suggested conformations appear as vertical and horizontal dashed lines—each marking a potential frame to extract.
Spacing Options
You have two main options to control how your conformations are picked:
- Number of conformations: The wizard selects an even number of conformations across the trajectory so they span the reaction coordinate effectively.
- Minimum COM spacing: The frames are selected to maintain a minimum center-of-mass distance between them, ensuring good sampling resolution along the reaction coordinate.
Note
You can also limit the start and end frames between which conformations are chosen, which helps if you’re only interested in a specific window along the coordinate.
What Happens After?
Clicking Generate project will create a batch project folder suffixed with _umbrella. This folder contains subfolders—one per selected conformation—as well as a frames.ndx file listing which trajectory frames were chosen. With this setup, you’re ready to move on to NPT equilibration and production MD simulations for each window.
Why It Matters
Automatically selecting a meaningful distribution of conformations along your reaction coordinate removes a subtle but important source of error. Spacing them too closely leads to redundant windows and wasted resources. Skipping key transition zones leads to gaps in your PMF. The GROMACS Wizard simplifies this process, offering both visual guidance and fine control over conformational spacing.
If you’re starting to set up umbrella sampling studies, this tool serves as a good checkpoint to ensure your setup is physically relevant—without requiring complex preprocessing scripts or external tools.
To learn more about this workflow, including options for creating conformations externally or performing PMF analysis, check out the complete Umbrella Sampling tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.