PLUMED contains a number of simple command line tools. To use one of these tools you issue a command something like:

plumed <toolname> <list of input flags for that tool>

The following is a list of the various standalone tools that PLUMED contains.

completion	Dumps the body of a bash function to be used for auto completion.
config	inquire plumed about how it was configure
driver	driver is a tool that allows one to to use plumed to post-process an existing trajectory.
driver-float	Equivalent to driver, but using single precision reals.
gen_example	gen_example is a tool that you can use to construct an example for the manual that users can interact with to understand
gen_json	gen_json constructs a json file that includes a dictionary of actions, the keywords for those actions and the components and outputs this to standard output
gentemplate	gentemplate is a tool that you can use to construct template inputs for the various actions
info	This tool allows you to obtain information about your plumed version
kt	Print out the value of k_B T at a particular temperature
manual	manual is a tool that you can use to construct the manual page fora particular action
mklib	compile a .cpp file into a shared library
newcv	create a new collective variable from a template
partial_tempering	scale parameters in a gromacs topology to implement solute or partial tempering
patch	patch an MD engine
pathtools	pathtools can be used to construct paths from pdb data
pdbrenumber	Modify atom numbers in a PDB, possibly using hybrid-36 coding.
pesmd	Pesmd allows one to do (biased) Langevin dynamics on a two-dimensional potential energy surface.
selector	create lists of serial atom numbers
simplemd	simplemd allows one to do molecular dynamics on systems of Lennard-Jones atoms.
sum_hills	sum_hills is a tool that allows one to to use plumed to post-process an existing hills/colvar file
vim2html	convert plumed input file to colored html using vim syntax

In addition to the keywords above, by enabling optional modules you can access to the following keywords:

drr_tool	(from Extended-System Adaptive Biasing Force module) - Extract .grad and .count files from the binary output .drrstate - Merge windows
ves_md_linearexpansion	(from Variationally Enhanced Sampling (VES code) module) Simple MD code for dynamics on a potential energy surface given by a linear basis set expansion.

For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file.