CLI Tutorials#
maize-biosimspace provides a large number of nodes for performing common operations such as parameterisation, minimisation, equilibration, production molecular
dynamics, and alchemical free energy calculations. Nodes are generally engine-specific as maize requires that nodes have a list of required_callables whose presence
in the environment is checked before the node is run. To see a list of all available nodes, type bss_ and hit tab to list them. To see the options for each, pass
pass the -h flag e.g.
bss_parameterise -h
These tutorials give specific examples of using BioSimSpace maize nodes to run production molecular dynamics, to create equilibrated systems starting from unparameterised input structures, and to run absolute binding free energy calculations starting from a protein pdb and an sdf file containing multiple ligands.