Studying molecular transitions—the steps a molecule takes between two states—is key to understanding biological processes, designing drugs, and optimizing materials. Transition path sampling and optimization methods, like the Parallel Nudged Elastic Band (P-NEB) approach in SAMSON, help researchers explore these transitions in detail. However, one common pain point arises during these calculations: the time it takes to optimize transitions from a set of conformations.
If you usually work with conformations, there’s good news: converting them into a path structure in SAMSON can significantly speed up your P-NEB computations—without compromising accuracy.
Conformations vs. Paths: What’s the Difference?
In SAMSON terminology:
- Conformations are snapshots of a system’s atomic positions. They’re like still images of a process.
- Paths are sequences of conformations forming a trajectory. Think of a path as an animation that shows how one structure morphs into another over time.
When you apply the P-NEB method to a set of conformations, SAMSON performs optimization on each conformation individually. This is flexible but time-consuming. In contrast, applying P-NEB to a path is more efficient because the data is already organized into a continuous trajectory. Behind the scenes, SAMSON utilizes this structure to streamline computations.
Tip
You can convert a set of conformations into a path by selecting them in the Document view, right-clicking, and choosing Conformation > Create path from conformations.
Why Performance Matters
For computational chemists and molecular modelers, simulation time can quickly add up—especially when testing systems repeatedly. Choosing the right data structure (conformations vs. path) may cut down on unnecessary overhead. For example, the optimization of a ligand transition out of a protein binding pocket via a path executes more swiftly than using the same number of conformations.
How to Use a Path with P-NEB
Once your path is ready, using it with the P-NEB extension is straightforward:
- In the Document view, select the path node.
- Open the P-NEB app from Home > Apps > All.
- Set your parameters:
- Spring constant:
1.00 - Number of loops:
100 - Interaction model:
Universal Force Field - Optimizer:
FIRE - Enable Parallel execution
- Spring constant:
- Click Run.
SAMSON will then optimize the path. When complete, a new optimized path appears in the Document view:
You can double-click the new path to animate the transition or inspect it in more detail. The app interface also displays a summary of computed energies and forces for each step of the path.
Bottom Line
If you’re consistently applying P-NEB to sets of conformations, try converting them into a path first. You may save both time and computational resources—especially helpful for larger molecular systems or when iterating through multiple trial optimizations.
To learn more and see the full step-by-step tutorial, visit the full documentation page at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.