Next: The Help menu Up: The View menu Previous: Animation Contents

##
Effective mode

This option allows one to visualize the results of a QHA analysis (see Section 4.2.4.12) as an animation of a selected effective mode coming out the analysis using VMD. To do so, VMD must be installed and the preferences variables vmd_path storing the path for VMD reader executable must be correctly set.

Pressing the Effective mode viewer button will pop up the dialog shown on figure 4.68

Figure 4.68: The dialog from where a the pseudo-trajectory associated to a selected effective can be animated using VMD

The following input fields controls the parameters necessary to visualize the animation through VMD:

- QHA input file
  Format: string
  Default: the name of the QHA analysis output file if one such file is already currently loaded. Nothing otherwise
  Description: this widget allows to select the name of the QHA analysis output file to visualize.

- Quasi-Harmonic mode
  Format: not an editable entry
  Default: no effective mode selected
  Description: this widget allows to select which combination of effective modes to visualize.

- Number of frames
  Format: strictly positive integer
  Default: 10 if one QHA file is currently loaded. Nothing otherwise
  Description: this widget allows to specify the number of frames the pseudo-trajectory should contain. Calling VMD from nMOLDYN is quite time-consuming, the entered value should not be too high.

- Amplitude
  Format: strictly positive float
  Default: 0.1 if one QHA file is currently loaded. Nothing otherwise
  Description: this widget allows to specify the amplitude in nm of the motion associated to the selected effective mode (see Eq. 4.109).

Pressing the OK button will run the animation, pressing the Cancel button will close the dialog.

Next: The Help menu Up: The View menu Previous: Animation Contents