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Load NetCDF file

The Load NetCDF file option allows one to select the NetCDF file of the trajectory which will be used to perform the analysis. Clicking on it, a file browser like the one showed in figure 4.2 pops up.

Figure 4.2: File-Directory selection window.

To select a directory, double click on it. By doing this, the complete pathname of the selected directory appears on the Directory selection button at the top of the window. To select the parent directory left-click the directory selection button. When a file in the list is highlighted (clicked) its name is shown in the File name field. The selection is confirmed by pressing the button Open of the browser. By doing this, the file selection window closes.

Two kind of files can be loaded in nMOLDYN, the MMTK NetCDF files and the MMTK trajectory set files (usually with respective .nc and .ncs extensions), the latter being just an ASCII file where each line is a link to a MMTK NetCDF file. The figure 4.3 shows an example of a trajectory set file.

Figure 4.3: Example of a MMTK trajectory set file.

For more details about trajectory set files, please refer to the MMTK documentation [47].

Please note again that the MMTK NetCDF file format is central to nMOLDYN as it is the only trajectory format that nMOLDYN can handle directly. Trajectories that have not been produced with MMTK or MMTK-based programs must be converted to MMTK format before they can be analyzed with nMOLDYN.

One important step that is performed by nMOLDYN when loading the trajectory is the determination of the chemical contents of the MMTK universe corresponding to the loaded trajectory. nMOLDYN attributes to each MMTK chemical object found in the universe a name that is either its MMTK database name if this object is referenced in the MMTK internal database otherwise its name will be its number of atoms appended to its chemical object type (respectively A, AC, M, NC, PC, P for Atom, AtomCluster, Molecule, NucleotideChain, PeptideChain, Protein chemical types.). In the seldom case where the system contains some isomers, nMOLDYN will distinguish them by appending to their name the suffix _iso' where is the number of the isomer. In order to retrieve to which isomer corresponds the nMOLDYN name, a PDB file whose name is the name of the isomer is created in the output file directory.

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