Chemical systems contain an enormous number atoms, which, in most cases makes it simply impossible for us to understand anything by monitoring the atom positions directly. Consequently, we introduce Collective variables (CVs) that describe the chemical processes we are interested in and monitor these simpler quantities instead. These CVs are used in many of the methods implemented in PLUMED - there values can be monitored using PRINT, Functions of them can be calculated or they can be analyzed or biased using the Analysis and Biasing methods implemented in PLUMED. Before doing any of these things however we first have to tell PLUMED how to calculate them.

The simplest collective variables that are implemented in PLUMED take in a set of atomic positions and output one or multiple scalar CV values. Information on these variables is given on the page entitled CV Documentation while information as to how sets of atoms can be selected can be found in the pages on Groups and Virtual Atoms. Please be aware that PLUMED contains implementations of many other collective variables but that the input for these variables may be less transparent when it is first encountered. In particular, the page on Distances from reference configurations describes the various ways that you can calculate the distance from a particular reference configuration. So you will find instructions on how to calculate the RMSD distance from the folded state of a protein here. Meanwhile, the page on Functions describes the various functions of collective variables that can be used in the code. This is a very powerful feature of PLUMED as you can use the Functions commands to calculate any function or combination of the simple collective variables listed on the page CV Documentation. Lastly the page on MultiColvar describes MultiColvars.
MultiColvars allow you to use many different colvars and allow us to implement all these collective variables without a large amount of code. For some things (e.g. DISTANCES GROUPA=1 GROUPB=2-100 LESS_THAN={RATIONAL R_0=3}) there are more computationally efficient options available in plumed (e.g. COORDINATION). However, MultiColvars are worth investigating as they provide a flexible syntax for many quite-complex CVs.