Many molecular modelers working with GROMACS face a recurring challenge when preparing Umbrella Sampling simulations: extracting and organizing suitable initial conformations from a trajectory. While this may seem like a straightforward preprocessing step, doing it repeatedly — and correctly — can be cumbersome and error-prone.
The GROMACS Wizard in SAMSON simplifies this workflow significantly, turning a potentially manual task into a reproducible and guided process. This post walks you through how to generate an Umbrella Sampling project based on existing GROMACS trajectories, directly inside SAMSON. If you’ve already run a COM pulling simulation, you’re in luck — SAMSON can automatically use these trajectories to suggest conformations.
Step 1: Load your trajectory
In the GROMACS Wizard, switch to the Umbrella Sampling tab. Then, select the input project. This automatically identifies the trajectory file within your project folder.
Step 2: Define the reaction coordinate
Next, define the reaction coordinate by selecting two index groups — for example, chain A and chain B. These are typically center of mass groups that you want to analyze with Umbrella Sampling.
Note: You can add your own custom index groups if your system requires it. This flexibility is especially helpful when analyzing less typical molecular setups.
Step 3: Explore and choose conformations
Based on the trajectory, SAMSON automatically generates and displays a reaction coordinate plot, showing distance vs time. Vertical and horizontal dashed lines represent potential initial conformations.
You have two main sampling strategies:
- Number of conformations: Space them equally along the reaction coordinate.
- Minimum COM spacing: Choose conformations so that the center of mass distance between frames exceeds a user-defined minimum.
You can also trim your sampling window by specifying custom start and end frames to focus only on the meaningful parts of your trajectory.
Step 4: Generate batch project
Click Generate Project. SAMSON creates a new batch folder with a timestamp and an _umbrella suffix. This contains subfolders with one simulation-ready project per initial conformation.
Additionally, a frames.ndx file saves the exact frame indices used — a detail that’s easy to overlook and incredibly useful for future analysis or reproducing the study.
Why this matters
By automatically visualizing the reaction coordinate, pre-selecting frames, and generating structured output directories, SAMSON eliminates the noise and allows researchers to stay focused on modeling and analysis. This structured approach minimizes errors and standardizes Umbrella Sampling project setup… with just a few clicks.
To learn more about each step and additional options like custom group definitions and parameter adjustments, see the full documentation: GROMACS Wizard – Umbrella Sampling tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.