Optimize transition paths with the Parallel Nudged Elastic Band method
The Nudged Elastic Band (NEB) method allows for finding saddle points and minimum energy paths between known conformations. The method optimizes a number of intermediate images along the path by finding the lowest possible energy for each image while maintaining equal spacing between neighboring images. This constrained optimization is done by adding spring forces.
The NEB method can be used, for example, to determine transition paths between already obtained structures corresponding to local energy minima (obtained using, e.g., the FIRE minimizer).
The P-NEB (Parallel Nudged Elastic Band) app implements the climbing image nudged elastic band (NEB) method 1.
The P-NEB app can be applied to both a path and a set of conformations.
Note
Conformations are SAMSON nodes that store the positions of a selected group of atoms. Conformations can be created by selecting atoms and clicking Edit > Conformation. If atoms are moved, double-clicking on a conformation in the document view restores the saved positions.
Paths are SAMSON nodes that store trajectories of a selected group of atoms. Paths are typically created by apps or loaded from trajectory files. Double-clicking on a path in the document view starts/stops moving atoms along the path.
Note
If you want to apply P-NEB to determine a path between two relaxed states of a given system, you first need to generate a sequence of conformations between them, for example with linear interpolation, or with other SAMSON Extensions, e.g.: Ligand Path Finder.
Requirements#
Load the input model#
In SAMSON, go to Home > Download and insert one of the following sample documents:
- https://www.samson-connect.net/documents/39260103-9a48-49db-9488-5573d5f1e7b0 - an example of a Zinc ligand unbinding trajectory (a smaller system for tests).
- https://www.samson-connect.net/documents/046f1acd-c799-40f6-8185-cb4847eff795 - a protein-ligand complex of Lactose permease (1PV7) and Thiodigalactosid (TDG) with unbinding paths obtained using the Ligand Path Finder tutorial.
This will load a document with this tutorial's sample from SAMSON Connect.
The goal of this tutorial is to improve these ligand unbinding pathways by applying P-NEB to them.
Start the P-NEB app#
Open the P-NEB app via Home > Apps > All > P-NEB 
. You can also find it in the Find everything.
The P-NEB app has the following settings:
- Spring constant: the spring coefficient. Enter 1.00.
- Number of loops: the number of optimisations of the transition path. Enter 100.
- Interaction model: the interaction model (force field) used to compute energies and forces. Select "Universal Force Field".
- Optimizer: the algorithm used to optimize the transition path. Select "FIRE".
- Climbing image method: if checked, the P-NEB app will use the climbing image strategy to find the saddle point. Leave this box unchecked for now. You can try again later with the box checked.
- Parallel execution: if checked, the P-NEB app will run in parallel (one thread per conformation). Check this box.
- Suffix name: the suffix used to name the final path or the set of generated conformations. Enter "NEB".
As noted above, the P-NEB app can be applied to either paths or groups of conformations.
Apply P-NEB to a path#
In the Document view (1), select a path node.
- Interface menu > Document view or , : Ctrl+1, : Cmd+1
Then, in the P-NEB app, click on the Run button.
The Universal Force Field (UFF) setup will ask whether to use existing bonds - choose to use existing bonds and click OK.
Then P-NEB initialization and computation will start.
You can see the computation progress in the status bar:
Once the optimisation is complete, a new path will appear in the Document view:
A summary of the computation is given in the interface of the P-NEB app:
You may now select the new path in the document and examine it with the Inspector (1). You can also double-click the path to start and stop its animation. If you right-click on a path, you can also access some of its options via Path > ....
- Interface menu > Inspector or , : Ctrl+3, : Cmd+3
Apply P-NEB to a set of conformations#
Note
For the same system, applying P-NEB to a set of conformations will take longer than directly applying P-NEB to a path (consisting of the same steps). So, prefer using a path.
You can combine conformations into a path by selecting them in the document and in the context menu clicking on Conformation > Create path from conformations.
In the Document view, select a set of conformations. Then, click on the Run button in the P-NEB app.
The Universal Force Field (UFF) setup will ask whether to use existing bonds - choose to use existing bonds and click OK.
Once the optimisation is done, a P-NEB produced set of conformations will appear in the Document view:
You can double-click on these conformations to modify the corresponding atoms' positions in the document.
If you have any questions or feedback, please use the SAMSON Connect Forum.