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NetCDF file format

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. The project homepage is hosted by the Unidata program at the University Corporation for Atmospheric Research (UCAR) [43]. They are also the chief source of NetCDF -based software, standards development, updates ...[44]. The format is an open standard.

The data format is self-describing. This means that there is a header which describes the layout of the rest of the file, in particular the data arrays, as well as arbitrary file metadata in the form of name/value attributes. The format is platform independent, with issues such as endianness being addressed in the software libraries. The data arrays are rectangular, not ragged, and stored in a simple and regular fashion that allows efficient subsetting.

nMOLDYN expects trajectories to be in NetCDF format and follow the conventions of MMTK. 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. This conversion is necessary because no other common trajectory format permits efficient access both to conformations at a given time and to one-atom trajectories for all times. In addition to providing such an access, the NetCDF format has several advantages that make it particularly suitable for archiving trajectories:

- compact files (binary storage);
- machine-independent format;
- fully self-contained, complete information about the system is stored in the trajectory file.

The conversion of the trajectories from different formats to the MMTK format can be made directly via the nMOLDYN graphical user interface (see Section 4.1.2).

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