Generating initial conformations for umbrella sampling can be time-consuming, especially for researchers who already have a simulation trajectory and want to reuse it efficiently. If you’re using SAMSON’s GROMACS Wizard, there’s a streamlined and visual way to set this up using an existing GROMACS trajectory. This approach minimizes manual preprocessing and guides you with built-in tools to define your reaction coordinates and select frames.
Here’s how you can get started if you already have a trajectory from, for example, a COM Pulling simulation:
Step 1: Load Your Project
Open the GROMACS Wizard in SAMSON and switch to the Umbrella Sampling tab. After choosing an input project, the tool will automatically detect the trajectory file from your project folder:
Step 2: Define the Reaction Coordinate
Specify your reaction coordinate by selecting two index groups. You can choose default groups or create custom index groups (useful for later analysis or simulation setup).
Step 3: Choose Spacing for Initial Conformations
A clear plot will show the distance vs. time along your chosen reaction coordinate. Overlaying dashed lines indicate the suggested initial conformations, and you can control how these are spaced:
- Number of conformations – lets you choose how many frames you want, evenly distributed along the coordinate.
- Minimum COM spacing – picks frames based on the center-of-mass distance to maintain spacing thresholds.
You can also set start and end frames for selection, offering even more control over which parts of your trajectory you use.
Step 4: Generate Batch Project
Click Generate Project and the Wizard will create a dedicated batch project folder. This folder includes individual projects for each selected initial conformation and a frames.ndx file summarizing the frame selection.
By leveraging the visual interface and automation in SAMSON’s GROMACS Wizard, setting up umbrella sampling becomes simpler and reproducible – particularly helpful when refining simulation parameters or iterating over multiple systems.
Learn more in the full SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.