A molecular transition path can look plausible at a glance and still contain awkward intermediate structures. Atoms may move unevenly from one state to the next, or the route may need relaxation under an interaction model. The Parallel Nudged Elastic Band (P-NEB) app in SAMSON is designed for this refinement step: it optimizes the intermediate images of a path while spring forces help keep neighboring states distributed along it.
The key distinction is that P-NEB improves a candidate path; it does not create the initial route for you. Start with a path or a sequence of conformations between the states you want to connect. If you still need to generate a route, the documentation points to tools such as Ligand Path Finder and Protein Path Finder. For two relaxed protein structures, ARAP interpolation is another option for creating an initial path.
Prepare the input before optimizing
In SAMSON, a path stores a trajectory for a selected group of atoms. A conformation stores positions for that group at one point in the route. P-NEB accepts either a path or a set of conformations, but if you have both representations of the same sequence, prefer the path: the tutorial notes that optimizing a set of conformations takes longer. You can combine selected conformations into a path through Conformation > Create path from conformations in the context menu.
Before starting, add the P-NEB extension and the FIRE state updater. Load a sample path or prepare your own, then open P-NEB from Home > Apps > All > P-NEB, or find it with the Find everything… search box.
Choose a straightforward first run
For the tutorial’s example setup, enter a spring constant of 1.00 and 100 loops. Select Universal Force Field as the interaction model and FIRE as the optimizer. Check Parallel execution to run one thread per conformation. Leave Climbing image method unchecked for the first optimization; the app also lets you try the climbing-image strategy in a later run when you want to locate a saddle point. Set the suffix to NEB so the output is easy to distinguish from the input.
In the Document view, select the path and click Run. When the Universal Force Field setup asks whether to use existing bonds, choose to use them and confirm. P-NEB will initialize and begin optimizing; progress is shown in the status bar.
Inspect the result, not just the completion message
When the calculation finishes, SAMSON adds a new path to the Document view. Keep the original available so you can compare the input route with the optimized result. Select the new path and inspect it with the Inspector, or double-click it to start and stop its animation. Right-clicking the path provides additional options under Path > ….
This comparison is an important part of the workflow: optimization changes the intermediate structures, so review the resulting route before using it in a subsequent analysis. P-NEB is a path-refinement method, not a substitute for generating a suitable starting route or checking whether the chosen model and endpoints are appropriate for your system.
For the complete tutorial, settings, and additional screenshots, see Optimize transition paths with the Parallel Nudged Elastic Band method.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.