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.
ALIGNED_MATRIX	MATRIX	Adjacency matrix in which two molecule are adjacent if they are within a certain cutoff and if they have the same orientation.
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	VOLUMES	This quantity can be used to calculate functions of the distribution of collectivevariables for the atoms that lie in a particular, user-specified part of of the cell.
AVERAGE	GRIDCALC	Calculate the ensemble average of a collective variable
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
CAVITY	VOLUMES	This quantity can be used to calculate functions of the distribution of collectivevariables for the atoms that lie in a box defined by the positions of four atoms.
CELL	COLVAR	Calculate the components of the simulation cell
CENTER_OF_MULTICOLVAR	VATOM	Calculate a a weighted average position based on the value of some multicolvar.
CENTER	VATOM	Calculate the center for a group of atoms, with arbitrary weights.
CLASSICAL_MDS	DIMRED	Create a low-dimensional projection of a trajectory using the classical multidimensionalscaling algorithm.
CLUSTER_DIAMETER	CONCOMP	Print out the diameter of one of the connected components
CLUSTER_DISTRIBUTION	CONCOMP	Calculate functions of the distribution of properties in your connected components.
CLUSTER_NATOMS	CONCOMP	Gives the number of atoms in the connected component
CLUSTER_PROPERTIES	CONCOMP	Calculate properties of the distribution of some quantities that are part of a connected component
CLUSTER_WITHSURFACE	MATRIXF	Take a connected component that was found using a clustering algorithm and create a new cluster that contains those atoms that are in the cluster together with those atoms that are within a certain cutoff of the cluster.
COLUMNSUMS	MATRIXF	Sum the columns of a contact matrix
COMBINE	FUNCTION	Calculate a polynomial combination of a set of other variables.
COMMITTOR	PRINTANALYSIS	Does a committor analysis.
COM	VATOM	Calculate the center of mass for a group of atoms.
CONSTANT	COLVAR	Return one or more constant quantitieswith or without derivatives.
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.
CONTACT_MATRIX	MATRIX	Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff.
CONVERT_TO_FES	GRIDANALYSIS	Convert a histogram, \(H(x)\), to a free energy surface using \(F(x) = -k_B T \ln H(x)\).
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 the backbone chemical shifts for a protein.
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.
DFSCLUSTERING	MATRIXF	Find the connected components of the matrix using the depth first search clustering algorithm.
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.
DISTANCE_FROM_CONTOUR	COLVAR	Calculate the perpendicular distance from a Willard-Chandler dividing surface.
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-float	TOOLS	Equivalent to driver, but using single precision reals.
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	PRINTANALYSIS	Dump selected atoms on a file.
DUMPCUBE	GRIDANALYSIS	Output a three dimensional grid using the Gaussian cube file format.
DUMPDERIVATIVES	PRINTANALYSIS	Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).
DUMPFORCES	PRINTANALYSIS	Dump the force acting on one of a values in a file.
DUMPGRID	GRIDANALYSIS	Output the function on the grid to a file with the PLUMED grid format.
DUMPMASSCHARGE	PRINTANALYSIS	Dump masses and charges on a selected file.
DUMPMULTICOLVAR	PRINTANALYSIS	Dump atom positions and multicolvar on a file.
DUMPPROJECTIONS	PRINTANALYSIS	Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).
EFFECTIVE_ENERGY_DRIFT	GENERIC	Print the effective energy drift described in Ref [29]
ENERGY	COLVAR	Calculate the total energy of the simulation box.
ENSEMBLE	FUNCTION	Calculates the replica averaging of a collective variable over multiple replicas.
ERMSD	COLVAR	Calculate eRMSD with respect to a reference structure.
EXTENDED_LAGRANGIAN	BIAS	Add extended Lagrangian.
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	Measure how similar the environment around atoms is to that found in a FCC structure.
FIND_CONTOUR_SURFACE	GRIDANALYSIS	Find an isocontour by searching along either the x, y or z direction.
FIND_CONTOUR	GRIDANALYSIS	Find an isocontour in a smooth function.
FIND_SPHERICAL_CONTOUR	GRIDANALYSIS	Find an isocontour in a three dimensional grid by searching over a Fibonacci sphere.
FIT_TO_TEMPLATE	GENERIC	This action is used to align a molecule to a template.
FIXEDATOM	VATOM	Add a virtual atom in a fixed position.
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.
FOURIER_TRANSFORM	GRIDANALYSIS	Compute the Discrete Fourier Transform (DFT) by means of FFTW of data stored on a 2D grid.
FRET	COLVAR	Calculate the FRET efficiency between a pair of atoms.The efficiency is calculated using the Forster relation:
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 asa histogram i a variety of ways. Therefore it is not expected that you use thisduring 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.
GRADIENT	MCOLVARF	Calculate the gradient of the average value of a multicolvar value
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.
HBOND_MATRIX	MATRIX	Adjacency matrix in which two atoms are adjacent if there is a hydrogen bond between them.
HISTOGRAM	GRIDCALC	Accumulate the average probability density along a few CVs from a trajectory.
INCLUDE	GENERIC	Includes an external input file, similar to "#include" in C preprocessor.
INCYLINDER	VOLUMES	This quantity can be used to calculate functions of the distribution of collectivevariables for the atoms that lie in a particular, user-specified part of of the cell.
info	TOOLS	This tool allows you to obtain information about your plumed version
INPLANEDISTANCES	MCOLVAR	Calculate distances in the plane perpendicular to an axis
INSPHERE	VOLUMES	This quantity can be used to calculate functions of the distribution of collectivevariables for the atoms that lie in a particular, user-specified part of of the cell.
INTERMOLECULARTORSIONS	MCOLVARF	Calculate torsions between axis of adjacent molecules
INTERPOLATE_GRID	GRIDANALYSIS	Interpolate a smooth function stored on a grid onto a grid with a smaller grid spacing.
JCOUPLING	COLVAR	Calculates \(^3J\) coupling constants for a dihedral angle.
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
LOCALENSEMBLE	FUNCTION	Calculates the average over multiple arguments.
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 fora 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.
METAINFERENCE	BIAS	Calculate the Metainference Score for a set of back calculated experimental data.
MFILTER_BETWEEN	MFILTERS	This action can be used to filter the colvar values calculated by a multicolvarso that one can compute the mean and so on for only those multicolvars within a certain range.
MFILTER_LESS	MFILTERS	This action can be used to filter the distribution of colvar values in a multicolvarso that one can compute the mean and so on for only those multicolvars less than a tolerance.
MFILTER_MORE	MFILTERS	This action can be used to filter the distribution of colvar values in a multicolvarso that one can compute the mean and so on for only those multicolvars more than a tolerance.
MOLECULES	MCOLVAR	Calculate the vectors connecting a pair of atoms in order to represent the orientation of a molecule.
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.
MTRANSFORM_BETWEEN	MTRANSFORMS	This action can be useed to transform the colvar values calculated by a multicolvar using a histogrambead
MTRANSFORM_LESS	MTRANSFORMS	This action can be useed to transform the colvar values calculated by a multicolvar using a switchingfunction
MTRANSFORM_MORE	MTRANSFORMS	This action can be useed to transform the colvar values calculated by a multicolvar using one minus a switchingfunction
MULTICOLVARDENS	GRIDCALC	Evaluate the average value of a multicolvar on a grid.
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 NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atomsor ambiguous NOE.
OUTPUT_CLUSTER	CONCOMP	Output the indices of the atoms in one of the clusters identified by a clustering object
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.
PBMETAD	BIAS	Used to performed Parallel Bias MetaDynamics.
PCARMSD	DCOLVAR	Calculate the PCA components ( see [58] and [56] ) for a number of provided eigenvectors and an average structure. Performs optimal alignment at every step and reports the rmsd so you know if you are far or close from the average structure.It takes the average structure and eigenvectors in form of a pdb.Note that beta and occupancy values in the pdb are neglected and all the weights are placed to 1 (differently from the RMSD colvar for example)
PCA	DIMRED	Perform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input.
PCAVARS	COLVAR	Projection on principal component eigenvectors or other high dimensional linear subspace
PIECEWISE	FUNCTION	Compute a piecewise straight line through its arguments that passes througha set of ordered control points.
PLANES	MCOLVAR	Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule.
POSITION	COLVAR	Calculate the components of the position of an atom.
PRE	COLVAR	Calculates the Paramegnetic Resonance Enhancement intensity ratio between two atoms.The reference atom for the spin label is added with SPINLABEL, the affected atom(s)are give as numbered GROUPA1, GROUPA2, ...The additional parameters needed for the calculation are given as INEPT, the inepttime, TAUC the correlation time, OMEGA, the larmor frequency and RTWO for the relaxationtime.
PRINT	PRINTANALYSIS	Print quantities to a file.
PROPERTYMAP	COLVAR	Calculate generic property maps.
PUCKERING	COLVAR	Calculate sugar pseudorotation coordinates.
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.
RESET_CELL	GENERIC	This action is used to rotate the full cell
RESTART	GENERIC	Activate restart.
RESTRAINT	BIAS	Adds harmonic and/or linear restraints on one or more variables.
REWEIGHT_BIAS	REWEIGHTING	Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored
REWEIGHT_METAD	REWEIGHTING	Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system.
REWEIGHT_TEMP	REWEIGHTING	Calculate weights for ensemble averages allow for the computing of ensemble averages at temperatures lower/higher than that used in your original simulation.
RMSD	DCOLVAR	Calculate the RMSD with respect to a reference structure.
ROWSUMS	MATRIXF	Sum the rows of a adjacency matrix.
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.
SMAC_MATRIX	MATRIX	Adjacency matrix in which two molecules are adjacent if they are within a certain cutoff and if the angle between them is within certain ranges.
SMAC	MCOLVARF	Calculate a variant on the SMAC collective variable discussed in [31]
SORT	FUNCTION	This function can be used to sort colvars according to their magnitudes.
SPRINT	MATRIXF	Calculate SPRINT topological variables from an adjacency matrix.
STATS	FUNCTION	Calculates statistical properties of a set of collective variables with respect to a set of reference values.In particular it calculates and store as components the sum of the squared deviations, the correlation, theslope and the intercept of a linear fit.
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 someset of collective variables.
TEMPLATE	COLVAR	This file provides a template for if you want to introduce a new CV.
TETRAHEDRALPORE	VOLUMES	This quantity can be used to calculate functions of the distribution of collective variablesfor the atoms lie that lie in a box defined by the positions of four atoms at the corners of a tetrahedron.
TETRAHEDRAL	MCOLVAR	Calculate the degree to which the environment about ions has a tetrahedral order.
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 theplumed.dat file. The same units must be used througout the plumed.dat file.
UPDATE_IF	PRINTANALYSIS	Conditional update of other actions.
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.
WRAPAROUND	GENERIC	Rebuild periodic boundary conditions around chosen atoms.
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.
XYDISTANCES	MCOLVAR	Calculate distance between a pair of atoms neglecting the z-component.You can then calculate functions of the distribution ofvalues such as the minimum, the number less than a certain quantity and so on.
XZDISTANCES	MCOLVAR	Calculate distance between a pair of atoms neglecting the y-component.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.
YZDISTANCES	MCOLVAR	Calculate distance between a pair of atoms neglecting the x-component.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.