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Parameters

Pressing the Root Mean-Square Displacement button will pop up the dialog shown on figure 4.36

Figure 4.36: The dialog from where the RMSD analysis will be set up and run.

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

- Trajectory file
  Format: Not an editable entry
  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 RMSD 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.

- Subset selection
  Format: subset selection string
  Default: all
  Description: this widget allows the selection of a subset of the system for the analysis. See Section 4.2.2.1 for more details.

- Deuteration selection
  Format: deuteration selection string
  Default: no
  Description: this widget allows the selection of a subset hydrogen atoms that will take the atomic parameters of deuterium. See Section 4.2.2.2 for more details.

- Weights
  Format: string equal to equal, mass, coherent, incoherent or atomicNumber
  Default: equal
  Description: this widget allows the selection of the weighting scheme to apply on each atomic contribution to the RMSD. See Section 4.2.1 for more details.

- RMSD output file
  Format: string
  Default: RMSD_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 RMSD analysis. A CDL version of the NetCDF output file is also automatically created with RMSD_traj_file.cdl name.

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