The following page contains an alphabetically ordered list of all the Actions and command line tools that are available in PLUMED 2. For lists of Actions classified in accordance with the particular tasks that are being performed see:

Full list of actions

ABMD	BIAS	Adds a ratchet-and-pawl like restraint on one or more variables.
ALPHABETA	COLVAR	Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values.
ALPHARMSD	COLVAR	Probe the alpha helical content of a protein structure.
ANGLES	MCOLVAR	Calculate functions of the distribution of angles .
ANGLE	COLVAR	Calculate an angle.
ANTIBETARMSD	COLVAR	Probe the antiparallel beta sheet content of your protein structure.
AROUND	MCOLVARF	This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.
BIASVALUE	BIAS	Takes the value of one variable and use it as a bias
BRIDGE	MCOLVAR	Calculate the number of atoms that bridge two parts of a structure
CELL	COLVAR	Calculate the components of the simulation cell
CENTER	VATOM	Calculate the center for a group of atoms, with arbitrary weights.
COMBINE	FUNCTION	Calculate a polynomial combination of a set of other variables.
COM	VATOM	Calculate the center of mass for a group of atoms.
CONSTANT	COLVAR	Return a constant quantity.
CONTACTMAP	COLVAR	Calculate the distances between a number of pairs of atoms and transform each distance by a switching function.The transformed distance can be compared with a set of reference values in order to calculate the squared distancebetween two contact maps.
COORDINATIONNUMBER	MCOLVAR	Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution ofcoordination numbers such as the minimum, the number less than a certain quantity and so on.
COORDINATION	COLVAR	Calculate coordination numbers.
CS2BACKBONE	COLVAR	This collective variable calculates a scoring function based on the comparison of backcalculated andexperimental backbone chemical shifts for a protein (CA, CB, C', H, HA, N).
DEBUG	GENERIC	Set some debug options.
DENSITY	MCOLVAR	Calculate functions of the density of atoms as a function of the box. This allows one to calculatethe number of atoms in half the box.
DHENERGY	COLVAR	Calculate Debye-Huckel interaction energy among GROUPA and GROUPB.
DIPOLE	COLVAR	Calcualte the dipole moment for a group of atoms.
DISTANCES	MCOLVAR	Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution ofdistances such as the minimum, the number less than a certain quantity and so on.
DISTANCE	COLVAR	Calculate the distance between a pair of atoms.By default the distance is computed taking into account periodicboundary conditions. This behavior can be changed with the NOPBC flag.Moreover, single components (x,y, and z) can be also computed.
driver	TOOLS	driver is a tool that allows one to to use plumed to post-process an existing trajectory.
DRMSD	COLVAR	Calculate the distance RMSD with respect to a reference structure.
DUMPATOMS	ANALYSIS	Dump selected atoms on a file.
DUMPDERIVATIVES	ANALYSIS	Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).
DUMPFORCES	ANALYSIS	Dump the force acting on one of a values in a file.
DUMPPROJECTIONS	ANALYSIS	Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).
ENERGY	COLVAR	Calculate the total energy of the simulation box.
EXTERNAL	BIAS	Calculate a restraint that is defined on a grid that is read during start up
FAKE	COLVAR	This is a fake colvar container used by cltools or various other actionsand just support input and period definition
FLUSH	GENERIC	This command instructs plumed to flush all the open files with a user specified frequency.Notice that all files are flushed anyway every 10000 steps.
FUNCPATHMSD	FUNCTION	This function calculates path collective variables.
FUNCSUMHILLS	FUNCTION	This function is intended to be called by the command line tool sum_hillsand it is meant to integrate a HILLS file or an HILLS file interpreted as a histogram i a variety of ways. Therefore it is not expected that you use this during your dynamics (it will crash!)
gentemplate	TOOLS	gentemplate is a tool that you can use to construct template inputs for the variousactions
GHOST	VATOM	Calculate the absolute position of a ghost atom with fixed coordinatesin the local reference frame formed by three atoms. The computed ghost atom is stored as a virtual atom that can be accessed inan atom list through the the label for the GHOST action that creates it.
GROUP	GENERIC	Define a group of atoms so that a particular list of atoms can be referenced with a single labelin definitions of CVs or virtual atoms.
GYRATION	COLVAR	Calculate the radius of gyration, or other properties related to it.
HISTOGRAM	ANALYSIS	Calculate the probability density as a function of a few CVs using kernel density estimation
IMD	GENERIC	Use interactive molecular dynamics with VMD
INCLUDE	GENERIC	Includes an external input file, similar to "#include" in C preprocessor.
info	TOOLS	This tool allows you to obtain information about your plumed version
LOAD	GENERIC	Loads a library, possibly defining new actions.
LOWER_WALLS	BIAS	The LOWER_WALLS and UPPER_WALLS keywords define a wall for the value of one or more collective variables, which limits the region of the phase space accessible during the simulation.
manual	TOOLS	manual is a tool that you can use to construct the manual page for a particular action
MATHEVAL	FUNCTION	Calculate a combination of variables using a matheval expression.
METAD	BIAS	Used to performed MetaDynamics on one or more collective variables.
MOLINFO	TOPOLOGY	This command is used to provide information on the molecules that are present in your system.
MOVINGRESTRAINT	BIAS	Add a time-dependent, harmonic restraint on one or more variables.
PARABETARMSD	COLVAR	Probe the parallel beta sheet content of your protein structure.
PATHMSD	COLVAR	This Colvar calculates path collective variables.
PIECEWISE	FUNCTION	Compute a piecewise straight line through its arguments that passes througha set of ordered control points.
PRINT	ANALYSIS	Print quantities to a file.
PROPERTYMAP	COLVAR	Calculate generic property maps.
RANDOM_EXCHANGES	GENERIC	Set random pattern for exchanges.
READ	GENERIC	Read quantities from a colvar file.
RESTART	GENERIC	Activate restart.
RESTRAINT	BIAS	Adds harmonic and/or linear restraints on one or more variables.
RMSD	COLVAR	Calculate the RMSD with respect to a reference structure.
simplemd	TOOLS	simplemd allows one to do molecular dynamics on systems of Lennard-Jones atoms.
SORT	FUNCTION	This function can be used to sort colvars according to their magnitudes.
sum_hills	TOOLS	sum_hills is a tool that allows one to to use plumed to post-process an existing hills/colvar file
TARGET	FUNCTION	This function measures the pythagorean distance from a particular structure measured in the space defined by some set of collective variables.
TEMPLATE	COLVAR	This file provides a template for if you want to introduce a new CV.
TIME	GENERIC	retrieve the time of the simulation to be used elsewere
TORSION	COLVAR	Calculate a torsional angle.
UNITS	GENERIC	This command sets the internal units for the code. A new unit can be set by eitherspecifying how to convert from the plumed default unit into that new unit or by usingthe shortcuts described below. This directive MUST appear at the BEGINNING of the plumed.dat file. The same units must be used througout the plumed.dat file.
UPPER_WALLS	BIAS	The LOWER_WALLS and UPPER_WALLS keywords define a wall for the value of one or more collective variables, which limits the region of the phase space accessible during the simulation.
VOLUME	COLVAR	Calculate the volume of the simulation box.
WHOLEMOLECULES	GENERIC	This action is used to rebuild molecules that can become split by the periodicboundary conditions.

Dictionary

BiasRepresentation	INTERNAL	An internal tool in plumed that is used to represent a bias
histogrambead	INTERNAL	A function that can be used to calculate whether quantities are between fixed upper and lower bounds.
kernelfunctions	INTERNAL	Functions that are used to construct histograms
reweighting	INTERNAL	Calculate free energies from a biassed/higher temperature trajectory.
switchingfunction	INTERNAL	Functions that measure whether values are less than a certain quantity.