For molecular modelers working with enhanced sampling techniques, one recurring challenge is selecting the right set of initial conformations for Umbrella Sampling simulations. Even experienced researchers can spend a significant amount of time manually extracting frames from long trajectories, calculating distances, and preparing data for batch simulations.
If you’ve ever wondered how to streamline the initial steps of umbrella sampling — especially when working from an existing GROMACS trajectory — this post is for you.
From Trajectory to Sampling Windows, All Within SAMSON
The GROMACS Wizard in SAMSON offers a clean, visual workflow to generate umbrella sampling projects, starting directly from your trajectory. The key advantage here is that the steps are integrated, consistent, and easy to follow.
Step 1: Load Your Project and Select Your Trajectory
Once inside the Umbrella Sampling tab of GROMACS Wizard, you begin by choosing your existing project folder, which contains the GROMACS trajectory you want to use. The trajectory is detected automatically, saving you a step.
Step 2: Specify the Reaction Coordinate
Next, you define the reaction coordinate by selecting two groups of atoms. These are typically index groups (e.g., chain A vs. chain B). If you need to, you can define custom index groups as well by following the link in the documentation.
Step 3: Fine-Tuning the Initial Conformations
This is where SAMSON really saves time. You have two options for spacing the initial conformations:
- Number of conformations: Generate evenly spaced snapshots along the reaction coordinate.
- Minimum COM spacing: Define conformations based on a minimum distance between centers of mass.
Once selected, you’ll see a preview of the reaction coordinate over time, with vertical lines indicating where initial conformations will be extracted. This gives you visual feedback before committing to the project generation.
Step 4: Generate Your Project
Click Generate project, and you’ll receive a timestamped folder with subfolders for each conformation and a frames.ndx file linking each configuration to the original trajectory. This output is ready for NPT equilibration and production MD simulations, which you can also manage directly within SAMSON in batch mode.
Why This Matters
In typical workflows, extracting initial conformations involves back-and-forth between visualization tools, index file modification, and scripting. With the GROMACS Wizard in SAMSON, these steps are visually integrated. Researchers can focus more on understanding the reaction coordinates and less on file management and script debugging.
Want to see all the options and steps? View the full umbrella sampling documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.