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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.
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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.
Next: Output
Up: Root Mean-Square Deviation
Previous: Theory and implementation
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pellegrini eric
2009-10-06