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:

Collective variables tells you about the ways that you can calculate functions of the positions of the atoms.
Analysis tells you about the various forms of analysis you can run on trajectories using PLUMED.
Bias tells you about the methods that you can use to bias molecular dynamics simulations with PLUMED.

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.
CH3SHIFTS	COLVAR	This collective variable calculates a scoring function based on the comparison of calculated andexperimental methyl chemical shifts.
CLASSICAL_MDS	ANALYSIS	Create a low-dimensional projection of a trajectory using the classical multidimensional scaling algorithm.
COMBINE	FUNCTION	Calculate a polynomial combination of a set of other variables.
COMMITTOR	ANALYSIS	Does a committor analysis.
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 reference value in order to calculate the squared distancebetween two contact maps. Each distance can also be weighted for a given value. CONTACTMAP can be used togetherwith FUNCPATHMSD to define a path in the contactmap space.
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.
DIHCOR	COLVAR	Measures the degree of similarity between dihedral angles.
DIPOLE	COLVAR	Calculate 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.
driver	TOOLS	driver is a tool that allows one to to use plumed to post-process an existing trajectory.
DRMSD	DCOLVAR	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.
DUMPMULTICOLVAR	ANALYSIS	Dump atom positions and multicolvar on 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.
ENSEMBLE	FUNCTION	Calculates the replica averaging of a collective variable over multiple replicas.
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
FCCUBIC	MCOLVAR
MOLECULES	MCOLVAR	Calculate the vectors connecting a pair of atoms in order to represent the orientation of a molecule.
FIT_TO_TEMPLATE	GENERIC	This action is used to align a molecule to a template.
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.
GPROPERTYMAP	COLVAR	Property maps but with a more flexible framework for the distance metric being used.
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 either using kernel density estimation, or a discretehistogram 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
kt	TOOLS	Print out the value of \(k_BT\) at a particular temperature
LOAD	GENERIC	Loads a library, possibly defining new actions.
LOCAL_AVERAGE	MCOLVARF	Calculate averages over spherical regions centered on atoms
LOCAL_Q3	MCOLVARF	Calculate the local degree of order around an atoms by taking the average dot product between the \(q_3\) vector on the central atom and the \(q_3\) vectoron the atoms in the first coordination sphere.
LOCAL_Q4	MCOLVARF	Calculate the local degree of order around an atoms by taking the average dot product between the \(q_4\) vector on the central atom and the \(q_4\) vectoron the atoms in the first coordination sphere.
LOCAL_Q6	MCOLVARF	Calculate the local degree of order around an atoms by taking the average dot product between the \(q_6\) vector on the central atom and the \(q_6\) vectoron the atoms in the first coordination sphere.
LOWER_WALLS	BIAS	Defines 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.
MULTI-RMSD	DCOLVAR	Calculate the RMSD distance moved by a number of separated domains from their positions in a reference structure.
NLINKS	MCOLVARF	Calculate number of pairs of atoms/molecules that are "linked"
NOE	COLVAR	Calculates the deviation of current distances from experimental NOE derived distances.
PARABETARMSD	COLVAR	Probe the parallel beta sheet content of your protein structure.
PATHMSD	COLVAR	This Colvar calculates path collective variables.
PATH	COLVAR	Path collective variables with a more flexible framework for the distance metric being used.
PIECEWISE	FUNCTION	Compute a piecewise straight line through its arguments that passes througha set of ordered control points.
POSITION	COLVAR	Calculate the components of the position of an atom.
PRINT	ANALYSIS	Print quantities to a file.
PROPERTYMAP	COLVAR	Calculate generic property maps.
Q3	MCOLVAR	Calculate 3rd order Steinhardt parameters.
Q4	MCOLVAR	Calculate 4th order Steinhardt parameters.
Q6	MCOLVAR	Calculate 6th order Steinhardt parameters.
RANDOM_EXCHANGES	GENERIC	Set random pattern for exchanges.
RDC	COLVAR	Calculates the Residual Dipolar Coupling between two atoms.
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	DCOLVAR	Calculate the RMSD with respect to a reference structure.
SIMPLECUBIC	MCOLVAR	Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simplecubic 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.
SPRINT	MCOLVARF	Calculate SPRINT topological variables.
sum_hills	TOOLS	sum_hills is a tool that allows one to to use plumed to post-process an existing hills/colvar file
TARGET	DCOLVAR	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.
TETRAHEDRAL	MCOLVAR
TIME	GENERIC	retrieve the time of the simulation to be used elsewere
TORSIONS	MCOLVAR	Calculate whether or not a set of torsional angles are within a particular range.
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	Defines a wall for the value of one or more collective variables, which limits the region of the phase space accessible during the simulation.
UWALLS	MCOLVARB	Add UPPER_WALLS restraints on all the multicolvar values
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.
XDISTANCES	MCOLVAR	Calculate the x components of the vectors connecting one or many pairs of atoms. You can then calculate functions of the distribution ofvalues such as the minimum, the number less than a certain quantity and so on.
YDISTANCES	MCOLVAR	Calculate the y components of the vectors connecting one or many pairs of atoms. You can then calculate functions of the distribution ofvalues such as the minimum, the number less than a certain quantity and so on.
ZDISTANCES	MCOLVAR	Calculate the z components of the vectors connecting one or many pairs of atoms. You can then calculate functions of the distribution ofvalues such as the minimum, the number less than a certain quantity and so on.