Getting Umbrella Sampling right often starts with one frustrating step: selecting meaningful initial conformations. Should you extract frames from a trajectory? Or start from a pathway of your own? How many conformations are enough? Picking them manually, or writing custom scripts to automate the process, can be time-consuming and error-prone.
Luckily, if you are using GROMACS Wizard inside SAMSON, the process becomes a lot more manageable and visually guided.
Two ways to start
When you want to perform Umbrella Sampling, you need a set of initial frames along the reaction coordinate. In GROMACS Wizard, you can:
- Use an existing GROMACS trajectory, such as one generated through COM pulling.
- Provide your own set of conformations or a path generated inside or outside SAMSON.
Visualizing and choosing conformations
Once your input is loaded, switch to the Umbrella Sampling tab. You’ll be prompted to select two index groups that define your reaction coordinate. GROMACS Wizard immediately plots the distance between the two groups over time. You’ll see vertical dashed lines that suggest good starting frames.
This quick visualization gives you confidence that you’re sampling the entire region of interest, without requiring extra scripting or manual inspection.
Flexible spacing options
Now comes the part that saves real time: choosing how the conformations are spaced.
- Number of conformations: The wizard will automatically distribute frames evenly along your reaction coordinate. Great when you know how many simulations your resources can handle.
- Minimum COM spacing: Choose this if you care about physical spacing. Conformations will be chosen so that the center of mass of your groups are at least a given distance apart.
Optionally, you can restrict the selection to a specific time range in your trajectory, making targeted, informed sampling even easier.
What happens next?
Once you click Generate Project, GROMACS Wizard organizes the conformations into a batch folder. Each conformation becomes a subproject, and you also get a frames.ndx file for traceability. Conveniently, all projects are ready for the next steps: equilibration, simulation, and PMF analysis.
Whether you’re sampling a simple ligand–protein distance or a complex path, this approach saves time and reduces the chances for mistakes. You get clarity, reproducibility, and understandable visual feedback along the way.
Learn more in the full tutorial here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/umbrella-sampling/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.