When modeling molecular systems, understanding how a molecule transitions from one conformation to another can be crucial. These transition paths often characterize reaction mechanisms, ligand unbinding, or conformational changes. However, extracting precise transition information can be computationally expensive and time-consuming, especially when using constrained optimization methods such as the NEB method.
The Parallel Nudged Elastic Band (P-NEB) method in SAMSON provides a powerful tool for identifying minimum energy paths and saddle points in a molecular system. But there’s an important detail that can make your experience significantly more efficient: whether you apply P-NEB to a set of conformations or directly to a path.
Why paths are usually better
SAMSON allows users to apply P-NEB to either a group of conformations or a path—it supports both. However, there’s a performance difference. If you’re looking to speed up your optimization while maintaining accuracy, choosing a path may just be your best option.
Key Tip
Prefer using paths. For the same system, applying P-NEB to a path is faster than applying it to a list of conformations.
What’s the difference?
Conformations are saved positions of selected atoms. They’re useful snapshots but exist as separate data entities. Applying P-NEB across multiple conformations takes more time, as each needs to be evaluated independently and sequentially.
Paths, on the other hand, are organized trajectories—a continuous structure of atomic motion. SAMSON can apply P-NEB more efficiently to paths because the continuity allows for parallel computation and tightly coupled optimization along the trajectory.
How to turn conformations into a path
Already have conformations? No need to discard them. In SAMSON, you can easily convert them into a path:
In the Document view, select your conformations. Then right-click to open the context menu, and choose Conformation > Create path from conformations.
This will generate a path node that can be immediately used with P-NEB. The entire process takes seconds and can save minutes—or even hours—of computational time, especially for large systems.
Optimizing with P-NEB
Once you’ve created a path, apply P-NEB via the Home > Apps > All > P-NEB menu, configure your parameters such as the number of iterations (e.g., 100 loops), force field (e.g., UFF), and optimizer (e.g., FIRE), then simply click Run.
After computation, you’ll see a new optimized transition path in the Document view. You can animate it, inspect it in detail, and continue refining it as needed. This optimized path provides a smoother and potentially more realistic transition between molecular states.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.