Chain Coordinate Plot
A Chain Coordinate Plot dialog is used to show plots of the energy (Heat of Formation) and RMS Gradient Norm of the energy versus a Chain coordinate for a series of molecules in a molecule group. This dialog is accessible if the parent view window's current molecule was loaded from an Ampac result file generated from an Ampac Chain calculation, and if the molecule has not been modified.
The Chain Coordinate Plot dialog for the active view window is opened and / or activated by selecting "Chain..." from the Results Menu of the main window or the context popup menu of the active view window.
While this dialog is open the current molecule in the parent view window is read-only, i.e., it cannot be modified, though it can be deleted from the molecule group. When a molecule is deleted from a group, its corresponding point on the plot is simply removed.
A Chain Coordinate Plot dialog is similar in appearance and functionality to a Reaction Path Plot dialog, though the meaning of the plots differs, of course.
See the Ampac Calculation Setup dialog and the Ampac Manual for details on how to set up Chain calculations and interpret the results.
The general features and usage of the Chain Coordinate Plot dialog can be found in Result Plots and Spectra. That section includes detailed information on manipulating the plots, such as showing / hiding, zooming, printing, and changing units. A specific example of chain coordinate plot is given below.
Figure 1. The Chain Coordinate Plot dialog (left) for the molecule group in the view window on the right. The active molecule is a transition state located by the Chain calculation.