The functionality in PLUMED 2 is divided into a small number of modules. Some users may only wish to use a subset of the functionality available within the code while others may wish to use some of PLUMED's more complicated features. For this reason the plumed source code is divided into modules, which users can activate or deactivate to their hearts content.
You can activate a module at configure time using the keyword --enable-modules. For example:

./configure --enable-modules=modulename

will enable module called modulename. A module that is on by default can be disabled using the following syntax

./configure --enable-modules=-modulename

To enable or disable multiple modules one should provide them as a : separated list. Notice that +modulename and modulename both activate the module, whereas -modulename deactivates it. E.g.

./configure --enable-modules=+crystallization:-colvar

will disable the colvar module and enable the crystallization module. Also notice that : can be omitted when using + or -. Thus, the same can be obtained with

./configure --enable-modules=+crystallization-colvar

If you repeat the --enable-modules keyword only the last instance will be used. Thus ./configure --enable-modules=crystallization --enable-modules=-colvar will not do what you expect!

There are also some shortcuts available:

./configure --enable-modules=all to enable all optional modules. This includes the maximum number of features in PLUMED, including modules that might not be properly functional.
./configure --enable-modules=none or ./configure --disable-modules to disable all optional modules. This produces a minimalistic PLUMED which can be used as a library but has no command line tools and no collective variables or biasing methods.
./configure --enable-modules=reset or ./configure --enable-modules to enable the default modules.

The two kinds of syntax can be combined and, for example, ./configure --enable-modules=none:colvar will result in a PLUMED with all the modules disabled with the exception of the colvar module.

Some modules are active by default in the version of PLUMED 2 that you download from the website while others are inactive. The following lists all of the modules that are available in plumed and tells you whether or not they are active by default.

Module name	Default behavior
adjmat	off
analysis	on
bias	on
cltools	on
colvar	on
crystallization	off
drr	off
eds	off
function	on
generic	on
isdb	on
manyrestraints	off
mapping	on
molfile	on
multicolvar	on
secondarystructure	on
setup	on
vatom	on
ves	off

Until PLUMED 2.2, it was also possible to switch on or off modules by adding files in the plumed2/src directory. Since PLUMED 2.3 this is discouraged, since any choice made in this manner will be overwritten next time ./configure is used.