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Parameters

Pressing the Rigid-Body Trajectory button will pop up the dialog shown on figure 4.43

Figure 4.43: The dialog from where the RBT analysis will be set up and run.

The following input fields controls the parameters for the RBT analysis:

- Trajectory file
  Format: string
  Default: traj_file where traj_file is the name of the loaded trajectory
  Description: the value of this widget can not be changed. It just recalls for information purpose the name of the trajectory file loaded for the analysis.

- Frame selection
  Format: string
  Default: 1:traj_length:1 where traj_length is the number of frames of the trajectory.
  Description: this widget allows to select the trajectory frames that will be used for the analysis. This must be a string of the form:
  first:last:step
  where first is an integer specifying the first frame number to consider, last is an integer specifying the last frame number to consider and step is an integer specifying the step number between two frames.

  For example,

  - 2:10:3 will select the frames 2, 5 and 8.
  - 1:5:1 will select the frames 1, 2, 3, 4 and 5.

- Reference frame
  Format: integer in [1,traj_length] where traj_length is the number of frames of the input trajectory
  Default: 1
  Description: this widget allows to specify which frame should be the reference for the RBT analysis. The value entered should be an integer ranging from 1 to traj_length where traj_length is the number of rames of the input trajectory.

- Remove translation
  Format: string equal to yes or no
  Default: no
  Description: if set to yes the translation motion will be removed from the RBT.

- Stepwise RBT
  Format: string equal to yes or no
  Default: no
  Description: if set to yes, each frame f will serve as the reference for the frame f+1 when defining the RBT canceling the value entred in Reference frame entry.

- Group selection
  Format: group selection string
  Default: all
  Description: this widget allows the selection of the groups of atoms that will be defined as rigid-bodies when performing the RBT. See Section 4.2.2.3 for more details.

- RBT output file
  Format: string
  Default: RBT_traj_file.nc where traj_file.nc is the name of the input trajectory
  Description: this widget allows to enter the name of the NetCDF output file of the RBT analysis.

Next: Output Up: Rigid-Body Trajectory Previous: Solution of the minimization Contents