Umbrella Sampling is a powerful technique for calculating free energy profiles along reaction coordinates, but setting it up can be time-consuming, especially when using data from existing trajectories. If you’re a molecular modeler with a finished GROMACS trajectory from a COM pulling simulation (or any other), you might be wondering—how can I reuse this without going through too much overhead?
In this post, we’ll walk through how SAMSON's GROMACS Wizard helps you quickly generate an umbrella sampling project directly from an existing GROMACS trajectory. This tutorial focuses on option 1: using a trajectory as your source of initial conformations.
Start with What You Already Have
If you've already completed a COM pulling simulation with GROMACS and have a trajectory (.xtc, .trr) ready, you can reuse this to extract conformations for umbrella sampling.
Within SAMSON, switch to the Umbrella Sampling tab in the GROMACS Wizard and select an input project. The software will automatically detect your trajectory file from the project folder.
Choose a Reaction Coordinate
To proceed, define your reaction coordinate by selecting two index groups—commonly, this could be the center-of-mass (COM) distance between two chains or domains.
You can also add custom index groups if needed. These can be useful not only for defining the reaction coordinate, but also for later analysis.
Visualize and Select Initial Conformations
Once your coordinate is selected, SAMSON will display a distance vs. time plot of the trajectory, showing suggested points that can serve as initial conformations. You have two options to define spacing:
- Number of conformations: Equally distributes conformations along the coordinate.
- Minimum COM spacing: Ensures a minimum physical separation between conformations.
Generate the Project
Once you are satisfied with the spacing, click Generate project. This creates a timestamped batch project folder with a _umbrella suffix. Inside, you'll find individual folders for each initial conformation. A frames.ndx file stores which frames were selected from the trajectory.
This setup simplifies what would otherwise require multiple manual steps. It helps reduce potential mistakes in coordinate selection, spacing, and file handling. If you're aiming to run PMF calculations, these steps take you well over halfway there.
To learn more and continue on with equilibration and PMF analysis, check out the full official documentation page for Umbrella Sampling in SAMSON:
Go to the complete Umbrella Sampling tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.