Usage

To use mdacli, after installation open your terminal and run:

mda -h

This command will provide a list of all available modules. A list of the Available modules is also available on the page of the documentation. Ask help -h in each module available for detailed instruction on how to use each module command-line client.

mdacli modules’ parameters emulate the parameters of the Analysis classes from MDAnalysis. So, each module will have its own requirements. Some will require two trajectories, others AtomGroup selections, etc. You will see that all is explained in each client -h option.

For example, to calculate a radial distribution function (RDF) between two groups use for example:

mda interrdf -h

A sample water trajectory is provided of rigid SPC/E water is provided online. topol.tpr contains a GROMACS topolgy file and traj.trr is the corresponding trajectory. The oxygen-oxygen rdf can be calculated using:

mda interrdf -s topol.tpr -f traj.trr -g1 "name OW" -g2 "name OW"

The oxygen atoms are selected with the -g1 and -g2 flags.

A more verbose output is achieved by using the -v flag. Even more information is provided with the --debug flag. All warnings of the run can also directly stored to a log file using the --logfile flag:

mda --debug --logfile rdf.log interrdf -v -s topol.tpr -f traj.trr -g1 "name OW" -g2 "name OW"

The results of each analysis are stored by default in the current directory. The output directory can be changed with the -o flag and an additional prefix can be set using the -pre flag.

The results of the RDF calculations are two .csv files. The actual RDF is saved in the 2nd and 3rd columns of InterRDF_count_bins_rdf.csv. The header rows of each file provide information about the stored data. Simple results such as bare numbers or strings are stored as JSON dumps. More complex data such as 4 or higher-dimensional arrays are saved as a bunch of CSV files zipped together. A similar procedure will happen for each module.