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Using nMOLDYNfrom the Graphical User Interface

Through the nMOLDYN graphical user interface, you will usually open a trajectory, then specify the parameters for the analysis you wish to perform and finally start the calculation itself. But you can also perform some other actions such as plotting the results of an analysis, performing some file conversions ...The graphical interface gives access to most of the functionalities of nMOLDYN. Moreover, from the graphical user interface it is possible to create an input file for the command-line interface or an autostart analysis python script. Both kind of files provide a convenient starting point to set up and run new analysis direclty from the command-line interface (see Section 5).
To run nMOLDYN from the GUI, type the following command line:
`python-dir/bin/nMOLDYNStart.py` on unix
or
`python-dir\Scripts\nMOLDYNStart.py` on Windows
python-dir being the prefix of your python distribution. The command line accepts some arguments that can change how nMOLDYN will start. The following arguments are currently supported by nMOLDYN:

- `-h/-help`
  Format: not an editable argument
  Value: None
  Description: displays the details of the command line arguments. Will not start nMOLDYN in GUI mode.

- `-version`
  Format: not an editable argument
  Value: None
  Description: displays the version of nMOLDYN. Will not start nMOLDYN in GUI mode.

- `-n/-netcdf=`
  Format: string
  Value: filename
  Description: starts nMOLDYN from the graphical user interface loading directly the filename NetCDF file.

- `-i/-input=`
  Format: string
  Value: filename
  Description: runs an analysis with the command-line interface using filename nMOLDYN input file (see Section 5.2 for details). Will not start nMOLDYN in GUI mode.

- `-c/-contents=`
  Format: string
  Value: filename molname selkwd
  Description: if file provided, displays the contents of the trajectory file file. If file and molname provided displays the selection keywords associated to molname. If file and molname and selkwd provided displays the selection values associated to selection keyword selkwd. Will not start nMOLDYN in GUI mode.

- `-t/-test=`
  Format: string
  Value: testname
  Description: runs one or several analysis benchmarks Will not start the GUI. The format for testname string is
  test1,test2,...
  where test1, test2 ...are the name of benchmark 1, 2 ... (see Section 4.4.4 for a comprehensive list of the available benchmarks).

- `-acroread_path=`
  Format: string
  Value: filename
  Description: sets the path for Acrobat Reader executable to filename. It will overide the preferences settings.

- `-vmd_path=`
  Format: string
  Value: filename
  Description: sets the path for VMD executable to filename. It will overide the preferences settings.

- `-documentation_style=`
  Format: string
  Value: html or pdf
  Description: sets the format for the online documentation either to HTML (html) either to pdf (pdf). It will overide the preferences settings.

- `-ncdump_path=`
  Format: string
  Value: filename
  Description: sets the path for ncdump executable to filename. It will overide the preferences settings.

- `-ncgen_path=`
  Format: string
  Value: filename
  Description: sets the path for ncgen executable to filename. It will overide the preferences settings.

- `-outputfile_path=`
  Format: string
  Value: dirname
  Description: sets the directory where all the output files will be written to dirname. It will overide the preferences settings.

- `-trajfile_path=`
  Format: string
  Value: dirname
  Description: sets the default MMTK trajectory input files directory search path to dirname. It will overide the preferences settings.

- `-warning_acroread=`
  Format: string
  Value: yes or no
  Description: if set to yes, will warn you if acrobat reader is not found on your system. It will overide the preferences settings.

- `-warning_ncdump=`
  Format: string
  Value: yes or no
  Description: if set to yes, will warn you if ncdump program is not found on your system. It will overide the preferences settings.

- `-warning_ncgen=`
  Format: string
  Value: yes or no
  Description: if set to yes, will warn you if ncgen program is not found on your system. It will overide the preferences settings.

- `-warning_vmd=`
  Format: string
  Value: yes or no
  Description: if set to yes, will warn you if VMD program is not found on your system. It will overide the preferences settings.

- `-progress_rate=`
  Format: integer in [0,100]
  Value: prog_rate
  Description: displays the progress of the analysis every prog_rate percents. It will overide the preferences settings.

When starting nMOLDYN from the GUI, the start-up window shown in figure 4.1 will pop up. This window contains four drop down menu buttons,

- File
- Analysis
- View
- Help

and a text window.

Figure 4.1: The nMOLDYN main window.

Everything concerning IO manipulations are done via the drop down menu button File. The drop down menu buttons Analysis allows to set up and start the analysis you are interested in. The View and Help buttons allow one to inspect input/output data and ask for help respectively. All of these menus will be described below.Finally, the text window will display all the information concerning the loaded file and the main actions performed on it.

Subsections

- The File menu
  - Load NetCDF file
  - Trajectory conversion
    - Amber to MMTK
    - CHARMM/X-PLOR to MMTK
    - DL_POLY to MMTK
    - Discover to MMTK
    - Forcite to MMTK
    - NAMD to MMTK
    - VASP to MMTK
  - Frame snapshot
  - Convert NetCDF to ASCII
  - Convert ASCII to NetCDF
  - Preferences
  - Quit
- The Analysis menu
  - Weighting scheme
  - Atom selection
    - Subset selection
      - selection from a selection file
      - selection from the loaded trajectory
      - selection from an expression string
    - Deuteration selection
      - selection from a selection file
      - selection from the loaded trajectory
      - selection from an expression string
    - Group selection
      - selection from a selection file
      - selection from the loaded trajectory
      - selection from an expression string
  - Running modes
  - The Dynamics menu
    - Mean-Square Displacement
      - Theory and implementation
      - Parameters
      - Output
    - Root Mean-Square Deviation
      - Theory and implementation
      - Parameters
      - Output
    - Radius of gyration
      - Theory and implementation
      - Parameters
      - Output
    - Angular Correlation
      - Theory and implementation
      - Parameters
      - Output
    - Velocity Autocorrelation Function
      - Theory and implementation
      - Parameters
      - Output
    - Density Of States
      - Theory and implementation
      - Parameters
      - Output
    - Pass-Band Filtered Trajectory
      - Theory and implementation
      - Parameters
      - Output
    - Global Motion Filtered Trajectory
      - Theory and implementation
      - Parameters
      - Output
    - Rigid-Body Trajectory
      - Theory and implementation
      - Parameters
      - Output
    - Center Of Mass Trajectory
      - Theory and implementation
      - Parameters
      - Output
    - Auto-Regressive Analysis
      - Theory and implementation
      - Parameters
      - Output
    - Quasi Harmonic Analysis
      - Theory and implementation
      - Parameters
      - Output
    - Reorientational Correlation Function
      - Theory and implementation
      - Parameters
      - Output
    - Angular Velocity AutoCorrelation Function
      - Theory and implementation
      - Parameters
      - Output
    - Angular Density Of States
      - Theory and implementation
      - Parameters
      - Output
  - The Scattering menu
    - Introduction
    - Dynamic Coherent Structure Factor
      - Theory and implementation
      - Parameters
      - Output
    - Dynamic Coherent Structure Factor (AR Model)
      - Theory and implementation
      - Parameters
      - Output
    - Dynamic Incoherent Structure Factor
      - Theory and implementation
      - Parameters
      - Output
    - Dynamic Incoherent Structure Factor (AR Model)
      - Theory and implementation
      - Parameters
      - Output
    - Dynamic Incoherent Structure Factor (Gaussian Approximation)
      - Theory and implementation
      - Parameters
      - Output
    - Elastic Incoherent Structure Factor
      - Theory and implementation
      - Parameters
      - Output
    - Static Coherent Structure Factor
      - Theory and implementation
      - Parameters
      - Output
    - Smoothed Static Coherent Structure Factor
      - Theory and implementation
      - Parameters
      - Output
  - The Structure menu
    - Pair Distribution Function
      - Theory and implementation
      - Parameters
      - Output
    - Coordination number
      - Theory and implementation
      - Parameters
      - Output
    - Spatial Density
      - Theory and implementation
      - Parameters
      - Output
    - ScrewFit analysis
      - Theory and implementation
      - Parameters
      - Output
  - The NMR menu
    - Order Parameter
      - Theory and implementation
      - Parameters
      - Output
    - Order Parameter (Contact Model)
      - Theory and implementation
      - Parameters
      - Output
- The View menu
  - Plot
  - Animation
  - Effective mode
- The Help menu
  - Documentation
  - Mailing List
  - API
  - Analysis benchmark
  - About nMOLDYN

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