For molecular modelers performing Umbrella Sampling, one of the early and often time-consuming hurdles is selecting the right set of initial conformations. This step significantly influences simulation efficiency and accuracy. If you’ve ever found yourself wondering how best to extract frames from a trajectory or how to distribute initial conformations along a reaction coordinate, the GROMACS Wizard in SAMSON offers a practical and visual workflow to help you do just that.
Common challenge: extracting good starting points
Umbrella Sampling requires multiple simulations centered around distinct configurations along a reaction coordinate. Generating these configurations often means manually selecting frames from a GROMACS trajectory or preparing them outside the platform entirely. Both options can be error-prone and cumbersome.
The GROMACS Wizard in SAMSON makes this step more manageable by letting you visually analyze your reaction coordinate and automatically generate evenly spaced conformations either by specifying how many you want, or by defining the spacing between them.
Using a GROMACS trajectory as input
Let’s say you’ve run a COM pulling simulation in GROMACS—perhaps to stretch a protein complex along the z-axis—and you’ve saved the trajectory. Instead of writing scripts or visually inspecting frames individually, you can import this trajectory into SAMSON’s Umbrella Sampling tab.
Here’s how to proceed:
- Select your input project: the Wizard auto-detects the trajectory.
- Define your reaction coordinate by choosing two index groups—e.g., chain A and chain B.
SAMSON then displays a reaction coordinate plot: distance vs time. Dashed lines indicate suggested frame selections, giving immediate visual feedback. This allows you to verify that the sampled region is appropriate before moving forward.
Specifying spacing options
You can then choose how your initial conformations are selected:
- By number of conformations — evenly distributes conformations along the distance profile.
- By minimum COM spacing — ensures a physical separation between configurations.
Want to avoid including noisy beginning or end frames? You can also specify start and end frames, giving you better control over the usable region of your trajectory.
One click to generate your project
After specifying the spacing, click Generate project, and SAMSON will create a batch project with a timestamp, containing individual subfolders for each initial conformation. You’ll also receive a frames.ndx file listing your selected frames for reproducibility and reference.
Conclusion
Setting up initial conformations for Umbrella Sampling doesn’t need to be a trial of scripting ability or a guessing game. With SAMSON’s GROMACS Wizard, you get a guided, visual process that keeps your setup efficient and traceable—making the rest of your simulations more effective down the line.
To learn more, refer to the full documentation here: 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 at https://www.samson-connect.net.