MDANSE Workflow

A typical computational workflow for most users goes through three main stages: (1) trajectory conversion, (2) analysis calculation and (3) results plotting.

1. Trajectory conversion

Before the trajectory can be analysed, it has to be converted to the MDANSE trajectory format (MDT). (Please read about MDANSE support for H5MD Files to find out about possible exceptions from this rule.)

Most likely your trajectory is in whatever format was output by your preferred Molecular Dynamics simulation software, and you need to convert it first. The converters will give you a chance to verify the information about the contents of the simulated system before you run the conversion. Once you have converted your trajectory to the MDANSE MDT format, you can use it as input for all analysis types. See also Trajectory Converters.

2a. Analysis parameters

Most analysis jobs offered by MDANSE are controlled by a number of input parameters which can be adjusted. MDANSE GUI typically attempts to fill all the fields with usable starting values, and highlights the invalid ones that need to be corrected by the user. We describe some of the more common parameters found in MDANSE below.

Frames

You can decide to limit the range of simulation frames used in the calculations, or to reduce the number of the frames taken in that range by increasing the step between them. Only the frames you selected will be passed to the analysis job. See also FramesConfigurator.

A more detailed discussion of the (correlation) frames can be found here: Time Series.

Atom selection

Just as it is not necessary to include all the time frames in the analysis, it is also possible to select only a subset of all the atoms present in the trajectory. Once you have defined a selection, you can run an analysis job on the selected atoms, and ignore the rest. This is useful if you are trying to determine which atoms contribute to a specific feature in your results. More details are given in the section Atom Selection.

Resolution

The resolution is enabled only for the analysis types which calculate an energy spectrum. This is normally applied to calculations involving Fourier transform of a correlation function (see also Fourier Spectrum). The resolution is applied by multiplying the time-dependent function with a window function before applying the Fourier transform. The details are given in the section Instrument resolution.

Weighting

The partial (usually by element) properties calculated can be combined using the weights chosen by the user, as described in the section Weighting Scheme. Please remember that the MDANSE_GUI normally recommends the weighting scheme appropriate to the type of analysis performed.

Output files

All the output arrays created in the analysis are written to the filesystem in the format chosen by the user. If you intend to continue visualising the results within the MDANSE_GUI, you will need to use the MDAFormat. If, however, you were planning to process the results further using other software, then you will need to pick the TextFormat output. See also Output files.

2b. Analysis results

The MDA files contain both the results and the original input parameters used to produce the results. In most cases, the output file will contain a total result, together with a number of partial datasets. The partial properties are typically grouped per atom type, or per pair of atom types. The relative contributions of different atoms to the total results will depend on the user’s choice of weights.

3. Plotting

If the MDAFormat was chosen for the analysis job output file, the file can then be opened in the MDANSE_GUI and plotted. As the MDANSE_GUI plotting is built on the matplotlib library many options found in the matplotlib are available in MDANSE_GUI. Additionally as the analysis calculations store unit information with results, MDANSE_GUI allows users to interactively switch between different units.

More information on plotting can be found in the section Plotting the Results.