normal modes
EasyHybrid also offers the capability of performing Normal Mode Analysis. In this section, we will focus on the technical aspects of the calculation within the interface, rather than the analysis of the results. For more information on running normal mode analysis in script form, please visit the Normal Modes section of the pDynamo homepage.
On the main toolbar, this is the icon that represents Normal Modes.
The normal modes calculations can also be performed by accessing:
Main Menu > Simulate > Normal Modes
An overview of the window for calculating Reaction coordinate scan can be seen in Figure 1.
Figure 1:Â The Normal Modes window.
Coordinates: These are the initial coordinates for the system.
Cycles: specifies for how many complete vibrational cycles structures should be calculated.
Frames Per Cycle: number of frames per cycle
Temperature: is the temperature, in kelvins, at which the trajectory is to be calculated.
Each normal mode will produce a trajectory in pDynamo's standard format, containing the designated number of frames per cycle. If the calculation was performed within EasyHybrid, the folder of each trajectory will also contain a log file with the wavenumber value of the respective vibration.