Preparing initial conformations for umbrella sampling can be a daunting process for molecular modelers, especially when dealing with long trajectories or custom paths. Selecting appropriate frames that are well-distributed along a reaction coordinate often requires scripting or external processing. Fortunately, the GROMACS Wizard in SAMSON offers a visual, intuitive way to streamline this setup.
Why it matters
Umbrella sampling requires initial conformations that span the space along a reaction coordinate—for example, a distance between two molecular groups. The quality of these initial states directly influences the accuracy of your Potential of Mean Force (PMF) calculations. Poor distribution or overlapping conformations can mean wasted resources, inconsistent sampling, or even inconclusive analyses.
A streamlined approach in SAMSON
Once you have your reaction coordinate defined—say, the separation between two chains—you can use the GROMACS Wizard to extract equidistributed conformations from your trajectory or path.
Selecting input
Load an existing project that contains your GROMACS trajectory. SAMSON automatically detects the trajectory file:
Define your reaction coordinate
Use two index groups (e.g., chain A and chain B) to define the distance-based coordinate:
You can also create custom index groups for added flexibility. These become especially useful during analysis or specialized pulling simulations.
Preview reaction coordinate evolution
Once selected, SAMSON displays a plot of distance vs time. Suggested initial conformations appear as dashed lines, letting you fine-tune your sampling strategy.
Two ways to choose conformations
- By number of conformations: Frames are spaced equally along the coordinate.
- By minimum center-of-mass (COM) spacing: Ensures that conformations are at least a certain distance apart.
You can even specify the start and end frames to restrict your selection to a region of interest. Once ready, click Generate project.
What you get
GROMACS Wizard generates a batch project folder that includes:
- One project per selected conformation
- A
frames.ndxfile listing chosen frames
This setup is ready for further steps: NPT equilibration, MD simulation, and eventually PMF computation using WHAM.
Rather than manually parsing trajectory files or writing scripts to extract frames, this intuitive interface saves time and reduces error—especially valuable when working with dozens of windows per region.
Learn more in the full Umbrella Sampling tutorial documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.