User guide

This guide is for people analysing their simulations with MolClusters, from the command line or from Python.

• Installation: install the molclusters command.
• Quick start: a first analysis, start to finish.
• How clusters are tracked: what a connection, a cluster and a cluster id are, and what the formation, split, merge and dissolution events mean. Worth reading before interpreting any result.
• Configuration: every key of the configuration file.
• Command line: the molclusters command's arguments and options.
• Output files: what each output file holds, column by column.
• The JSON report: the full per-frame, per-cluster record, and how to read it back.
• Cluster properties: how radius, density, dipole moment, sphericity and the other properties are computed, and their units.
• LAMMPS systems: residue names, elements and times for LAMMPS topologies and dumps.
• Using it from Python: run an analysis from a script or notebook and get the results as arrays and tables.
• Writing your own analysis: add per-frame analyses of your own.
• Troubleshooting: common errors and warnings, and what to do about them.
• Known issues in earlier versions: errors in v0.6.0 and earlier, the outputs they affect, and how to correct old results.