bALA tutorial

This tutorial is inspired by the classic pDynamo tutorial example for dALA (blocked alanine). You can find more information by visiting the official pDynamo page and referring to the book.

Step 1 - Open the EasyHybrid interface.

Step 2 - Load the blocked alanine system (bALA), whose coordinates are available for download here. To do this, in the window for importing new systems, select the OPLS force field and load the file bALA_not_opt.mol.

Step 3 - Geometry optimization.

Step 4 - Visual inspection of the optimized geometry and selection of the reaction coordinates for the potential energy surface (PES) scan.

Select the Oxygen and Hydrogen atoms that form a hydrogen bond, as shown in the figure below. To do this, you must use the "Picking" selection mode.

Step 5 - Open the PES tool window and import the data from the Picking selection by clicking the "Import from Picking Selections" button. This procedure will automatically load the data of the atoms associated with the chosen reaction coordinate. Set the number of steps to 20 and use an interval of 0.2 Ångströms between steps. Then, click Run to start the scan.

Step 6 - The scan should generate a new visualizable object that shows the stretched bALA (this is the last structure generated by the scanning process).

To visualize the trajectory and the obtained potential energy profile, right-click on the header of the system of interest in the Tree View of the main window and select Import Data. In the data import window, select the second format pkl folder - pDynamo trajectory. EasyHybrid will automatically detect that there is a log file associated with the obtained scan. Import the data – a new visualizable object will be generated, and you will notice it contains 20 frames, as it represents a trajectory.

Step 7 - Trajectory and PES inspection.

Go to Analyses and click on PES Analysis. A new window with an interactive PES graph should appear. You can explore which structures are associated with a given energy by adjusting the scrollbar at the bottom of the graph.