When setting up an umbrella sampling simulation, one of the early and critical steps is selecting a proper set of initial conformations. Doing this manually from a trajectory can be tedious and error-prone, especially if you’re unsure how to space them properly along the reaction coordinate. If you’ve ever asked yourself how many conformations you need, what spacing is appropriate, or how to organize the resulting simulations, you’re not alone.
The GROMACS Wizard in SAMSON provides a streamlined solution designed to make this step more intuitive and automated. This is particularly helpful if you already have a GROMACS trajectory, for example, from a center-of-mass (COM) pulling simulation, and you want to extract frames from it to serve as initial states for umbrella sampling.
What does it do for you?
In the Umbrella Sampling tab of the GROMACS Wizard, you start by choosing your project containing the trajectory. The wizard intelligently identifies the trajectory file, simplifying data selection.
Next, you specify the reaction coordinate by selecting two index groups, e.g., chain A and chain B. A plot of distance vs. time is automatically generated, with suggested initial conformation points marked. This visualization helps you understand how the reaction coordinate evolves and where to pick meaningful frames for sampling.
How to select conformations
You have two structured ways to define spacing between initial conformations:
- Number of conformations – Equidistant selection along the reaction coordinate.
- Minimum COM spacing – Ensures a minimum distance between selected positions.
For example, if you’re unsure how many frames are sufficient, just specify a desired COM spacing, and the wizard picks conformations with that minimum distance.
Or, if you know how many windows you want to run, you can distribute frames evenly with that count.
Automated organization
Once spacing is defined, clicking Generate project creates a structured batch folder. Each subfolder corresponds to one initial conformation—each ready to be initialized and run for equilibration and production simulations. A helpful frames.ndx file is also generated, recording which trajectory frames are used.
Why this matters
Not having to manually scan your trajectory and extract individual conformations saves time and helps you avoid inconsistencies. Equally important, keeping everything organized in a timestamped batch project reduces the overhead of tracking multiple simulations.
Especially in research or teaching labs, where reproducibility and clarity are vital, this feature from the GROMACS Wizard lowers the barrier to entry for robust sampling workflows.
To learn more about how to go from trajectory to PMF analysis, visit the full tutorial: https://documentation.samson-connect.net/tutorials/gromacs-wizard/umbrella-sampling/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.