Actions implemented in PLUMED Version 2.11
The actions that can be used within a PLUMED input file are listed below.
VES_TARGETDIST
VES_OPTIMIZER
ISDB_COLVAR
MCOLVARF
MATRIXF
VATOM
MATRIX
DIMRED
REWEIGHTING
GRIDANALYSIS
GRIDCALC
MAZE_LOSS_FUNCTION
COLVAR
ISDB_FUNCTION
PRINTANALYSIS
MCOLVAR
BIAS
MAZE_BIAS
DCOLVAR
VOLUMES
VES_BIAS
MAZE_OPTIMIZER
ISDB_GENERIC
ISDB_BIAS
FUNCTION
VES_UTILS
VES_BASISF
OPES_EXPANSION_CV
CONCOMP
GENERIC
EABFMOD_BIAS
LANDMARKS
TOPOLOGY
ANALYSIS
ANNMOD_Function
| Name | Description | Tags |
|---|---|---|
| ABMD | Adds a ratchet-and-pawl like restraint on one or more variables. | BIAS |
| ACCUMULATE | Sum the elements of this value over the course of the trajectory | GRIDCALC |
| ADAPTIVE_PATH | Compute path collective variables that adapt to the lowest free energy path connecting states A and B. | COLVAR |
| ALPHABETA | Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. | MCOLVAR |
| ALPHARMSD | Probe the alpha helical content of a protein structure. | COLVAR |
| ANGLE | Calculate one or multiple angle/s. | COLVAR |
| ANGLES | Calculate functions of the distribution of angles. | COLVAR |
| ANN | Calculates the ANN-function. | ANNMOD_Function |
| ANTIBETARMSD | Probe the antiparallel beta sheet content of your protein structure. | COLVAR |
| ARGS2VATOM | Create a virtual atom from the input scalars | VATOM |
| AROUND | 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. | VOLUMES |
| ARRANGE_POINTS | Arrange points in a low dimensional space so that the (transformed) distances between points in the low dimensional space match the dissimilarities provided in an input matrix. | DIMRED |
| ATOMIC_SMAC | Calculate the atomic smac CV | MCOLVAR |
| AVERAGE | Calculate the ensemble average of a collective variable | GRIDCALC |
| AVERAGE_PATH_DISPLACEMENT | Accumulate the distances between the reference frames in the paths and the configurations visited | ANALYSIS |
| BESSEL | Calculate the value of a Bessel function. | FUNCTION |
| BETWEEN | Use a switching function to determine how many of the input variables are within a certain range. | FUNCTION |
| BF_CHEBYSHEV | Chebyshev polynomial basis functions. | VES_BASISF |
| BF_COMBINED | Combining other basis functions types | VES_BASISF |
| BF_COSINE | Fourier cosine basis functions. | VES_BASISF |
| BF_CUBIC_B_SPLINES | Cubic B spline basis functions. | VES_BASISF |
| BF_CUSTOM | Basis functions given by arbitrary mathematical expressions. | VES_BASISF |
| BF_FOURIER | Fourier basis functions. | VES_BASISF |
| BF_GAUSSIANS | Gaussian basis functions. | VES_BASISF |
| BF_LEGENDRE | Legendre polynomials basis functions. | VES_BASISF |
| BF_POWERS | Polynomial power basis functions. | VES_BASISF |
| BF_SINE | Fourier sine basis functions. | VES_BASISF |
| BF_WAVELETS | Daubechies Wavelets basis functions. | VES_BASISF |
| BIASVALUE | Takes the value of one variable and use it as a bias | BIAS |
| BOPS | Calculate Bond orientational order parameters for molecules. | COLVAR |
| BRIDGE | Calculate a matrix with elements equal to one if there is a bridging atom between the two atoms | MCOLVAR |
| BRIDGE_MATRIX | Calculate the number of atoms that bridge two parts of a structure | MCOLVAR |
| CALIBER | Add a time-dependent, harmonic restraint on one or more variables. | ISDB_BIAS |
| CAVITY | This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a box defined by the positions of four atoms. | VOLUMES |
| CELL | Get the components of the simulation cell | COLVAR |
| CENTER | Calculate the center for a group of atoms, with arbitrary weights. | VATOM |
| CHARGE | Get the charges of one or multiple atoms | MCOLVAR |
| CLASSICAL_MDS | Create a low-dimensional projection of a trajectory using the classical multidimensional | DIMRED |
| CLUSTER_DIAMETER | Print out the diameter of one of the connected components. | CONCOMP |
| CLUSTER_DISTRIBUTION | Calculate functions of the distribution of properties in your connected components. | CONCOMP |
| CLUSTER_NATOMS | Calculate the number of atoms in the cluster of interest | CONCOMP |
| CLUSTER_PROPERTIES | Calculate properties of the distribution of some quantities that are part of a connected component | CONCOMP |
| CLUSTER_WEIGHTS | Setup a vector that has one for all the atoms that form part of the cluster of interest and that has zero for all other atoms. | CONCOMP |
| CLUSTER_WITHSURFACE | Determine the atoms that are within a certain cutoff of the atoms in a cluster. | CONCOMP |
| COLLECT | Collect data from the trajectory for later analysis | ANALYSIS |
| COLLECT_FRAMES | Collect atomic positions or argument values from the trajectory for later analysis | ANALYSIS |
| COM | Calculate the center of mass for a group of atoms. | VATOM |
| COMBINE | Calculate a polynomial combination of a set of other variables. | FUNCTION |
| COMMITTOR | Does a committor analysis. | PRINTANALYSIS |
| CONCATENATE | Join vectors or matrices together | MCOLVAR |
| CONSTANT | Create a constant value that can be passed to actions | COLVAR |
| CONTACTMAP | Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. | COLVAR |
| CONTACT_MATRIX | Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. | MATRIX |
| CONVERT_TO_FES | Convert a histogram to a free energy surface. | GRIDANALYSIS |
| COORDINATION | Calculate coordination numbers. | COLVAR |
| COORDINATIONNUMBER | Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of | MCOLVAR |
| COORDINATION_MOMENTS | Calculate moments of the distribution of distances in the first coordination sphere | MCOLVAR |
| COORDINATION_SHELL_AVERAGE | Calculate an arbitrary function of all the bond vectors in the first coordination sphere of an atom and take an average | MCOLVAR |
| COORDINATION_SHELL_FUNCTION | Calculate an arbitrary function of all the bond vectors in the first coordination sphere of an atom | MCOLVAR |
| COORD_ANGLES | Calculate functions of the distribution of angles between bonds in the first coordination spheres of a set of atoms | MCOLVAR |
| COVARIANCE_MATRIX | Calculate a covariance matix | REWEIGHTING |
| CREATE_MASK | Create a mask vector to use for landmark selection | DIMRED |
| CS2BACKBONE | Calculates the backbone chemical shifts for a protein. | ISDB_COLVAR |
| CUSTOM | Calculate a combination of variables using a custom expression. | FUNCTION |
| CYLINDRICAL_HARMONIC | Calculate the cylindrical harmonic function | MCOLVAR |
| DEBUG | Set some debug options. | GENERIC |
| DENSITY | Depreciated command that is bascially equivalant to GROUP. | MCOLVAR |
| DETERMINANT | Calculate the determinant of a matrix | MCOLVAR |
| DFSCLUSTERING | Find the connected components of the matrix using the depth first search clustering algorithm. | MATRIXF |
| DHENERGY | Calculate Debye-Huckel interaction energy between the atoms in GROUPA and GROUPB. | COLVAR |
| DIAGONALIZE | Calculate the eigenvalues and eigenvectors of a square matrix | ANALYSIS |
| DIFFERENCE | Calculate the differences between two scalars or vectors | FUNCTION |
| DIHCOR | Measures the degree of similarity between dihedral angles. | COLVAR |
| DIHEDRAL_CORRELATION | Measure the correlation between a pair of dihedral angles | COLVAR |
| DIMER | This CV computes the dimer interaction energy for a collection of dimers. | COLVAR |
| DIPOLE | Calculate the dipole moment for a group of atoms. | COLVAR |
| DISPLACEMENT | Calculate the displacement vector between the pair of input vectors | MCOLVAR |
| DISSIMILARITIES | Calculate the matrix of dissimilarities between a trajectory of atomic configurations. | ANALYSIS |
| DISTANCE | Calculate the distance/s between pairs of atoms. | COLVAR |
| DISTANCES | Calculate the distances between multiple piars of atoms | MCOLVAR |
| DISTANCE_FROM_CONTOUR | Calculate the perpendicular distance from a Willard-Chandler dividing surface. | COLVAR |
| DISTANCE_FROM_SPHERICAL_CONTOUR | Calculate the perpendicular distance from a Willard-Chandler dividing surface. | COLVAR |
| DISTANCE_MATRIX | Calculate a matrix of distances between atoms. | MATRIX |
| DOMAIN_DECOMPOSITION | Pass domain decomposed properties of atoms to PLUMED | ANALYSIS |
| DOPS | Calculate DOPS order parameter for molecules. | COLVAR |
| DRMSD | Calculate the distance RMSD with respect to a reference structure. | DCOLVAR |
| DRR | Used to performed extended-system adaptive biasing force (eABF) | EABFMOD_BIAS |
| DUMPATOMS | Dump selected atoms on a file. | PRINTANALYSIS |
| DUMPCONTOUR | Print the contour | GRIDANALYSIS |
| DUMPCUBE | Output a three dimensional grid using the Gaussian cube file format. | GRIDANALYSIS |
| DUMPDERIVATIVES | Dump the derivatives with respect to the input parameters for scalar values (generally CVs, functions or biases). | PRINTANALYSIS |
| DUMPFORCES | Dump the force acting on one of a values in a file. | PRINTANALYSIS |
| DUMPGRID | Output the function on the grid to a file with the PLUMED grid format. | GRIDANALYSIS |
| DUMPMASSCHARGE | Dump masses and charges on a selected file. | PRINTANALYSIS |
| DUMPMULTICOLVAR | Dump atom positions and a vector of values to a file. | MCOLVAR |
| DUMPPDB | Output PDB file. | PRINTANALYSIS |
| DUMPPROJECTIONS | Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). | PRINTANALYSIS |
| DUMPVECTOR | Print a vector to a file | PRINTANALYSIS |
| ECV_CUSTOM | Use some given CVs as a set of expansion collective variables (ECVs). | OPES_EXPANSION_CV |
| ECV_LINEAR | Linear expansion, according to a parameter lambda. | OPES_EXPANSION_CV |
| ECV_MULTITHERMAL | Expand a simulation to sample multiple temperatures simultaneously. | OPES_EXPANSION_CV |
| ECV_MULTITHERMAL_MULTIBARIC | Expand a simulation to sample multiple temperatures and pressures. | OPES_EXPANSION_CV |
| ECV_UMBRELLAS_FILE | Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. | OPES_EXPANSION_CV |
| ECV_UMBRELLAS_LINE | Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. | OPES_EXPANSION_CV |
| EDS | Add a linear bias on a set of observables. | BIAS |
| EEFSOLV | Calculates EEF1 solvation free energy for a group of atoms. | COLVAR |
| EFFECTIVE_ENERGY_DRIFT | Print the effective energy drift | GENERIC |
| EMMI | Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. | ISDB_COLVAR |
| EMMIVOX | Bayesian single-structure and ensemble refinement with cryo-EM maps. | ISDB_COLVAR |
| ENDPLUMED | Terminate plumed input. | GENERIC |
| ENERGY | Calculate the total potential energy of the simulation box. | COLVAR |
| ENSEMBLE | Calculates the replica averaging of a collective variable over multiple replicas. | FUNCTION |
| ENVIRONMENTSIMILARITY | Measure how similar the environment around atoms is to that found in some reference crystal structure. | MCOLVAR |
| ERMSD | Calculate eRMSD with respect to a reference structure. | COLVAR |
| EUCLIDEAN_DISTANCE | Calculate the euclidean distance between two vectors of arguments | MCOLVAR |
| EVALUATE_FUNCTION_FROM_GRID | Calculate the function stored on the input grid at an arbitrary point | GRIDANALYSIS |
| EXTENDED_LAGRANGIAN | Add extended Lagrangian. | BIAS |
| EXTERNAL | Calculate a restraint that is defined on a grid that is read during start up | BIAS |
| EXTRACV | Allow PLUMED to use collective variables computed in the MD engine. | COLVAR |
| FAKE | This is a fake colvar container that is used by cltools or various other actions that supports input and period definitions | COLVAR |
| FARTHEST_POINT_SAMPLING | Select a set of landmarks using farthest point sampling. | LANDMARKS |
| FCCUBIC | Measure how similar the environment around atoms is to that found in a FCC structure. | MCOLVAR |
| FCCUBIC_FUNC | Measure how similar the environment around atoms is to that found in a FCC structure. | MCOLVAR |
| FIND_CONTOUR | Find an isocontour in a smooth function. | GRIDANALYSIS |
| FIND_CONTOUR_SURFACE | Find an isocontour by searching along either the x, y or z direction. | GRIDANALYSIS |
| FIND_GRID_MAXIMUM | Find the point with the highest value of the function on the grid | GRIDANALYSIS |
| FIND_GRID_MINIMUM | Find the point with the lowest value of the function on the grid | GRIDANALYSIS |
| FIND_SPHERICAL_CONTOUR | Find an isocontour in a three dimensional grid by searching over a Fibonacci sphere. | GRIDANALYSIS |
| FISST | Compute and apply the optimal linear force on an observable to enhance sampling of conformational distributions over a range of applied forces. | BIAS |
| FIT_TO_TEMPLATE | This action is used to align a molecule to a template. | GENERIC |
| FIXEDATOM | Add a virtual atom in a fixed position. | VATOM |
| FLATTEN | Convert a matrix into a vector | FUNCTION |
| FLUSH | This command instructs plumed to flush all the open files with a user specified frequency. | GENERIC |
| FOURIER_TRANSFORM | Compute the Discrete Fourier Transform (DFT) by means of FFTW of data stored on a 2D grid. | GRIDANALYSIS |
| FRET | Calculates the FRET efficiency between a pair of atoms. | ISDB_COLVAR |
| FUNCPATHGENERAL | This function calculates path collective variables (PCVs) using an arbitrary combination of collective variables. | FUNCTION |
| FUNCPATHMSD | This function calculates path collective variables. | FUNCTION |
| FUNCSUMHILLS | This function is intended to be called by the command line tool sum_hills. It is meant to integrate a HILLS file or an HILLS file interpreted as a histogram in a variety of ways. It is, therefore, not expected that you use this during your dynamics (it will crash!) | FUNCTION |
| FUNNEL | Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. | BIAS |
| FUNNEL_PS | FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. | COLVAR |
| FUSIONPOREEXPANSIONP | A CV for inducing the expansion of a fusion pore from a nucleated fusion pore. | COLVAR |
| FUSIONPORENUCLEATIONP | A CV for inducing the nucleation of the fusion pore from a hemifusion stalk. | COLVAR |
| GATHER_REPLICAS | Create a vector that contains the copies of the input quantities from all replicas | ANALYSIS |
| GEOMETRIC_PATH | Distance along and from a path calculated using geometric formulas | COLVAR |
| GET | Get data from PLUMED for another code | ANALYSIS |
| GHBFIX | Calculate the GHBFIX interaction energy between GROUPA and GROUPB | COLVAR |
| GHOST | Calculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. | VATOM |
| GPATH | Distance along and from a path calculated using geometric formulas | COLVAR |
| GPROPERTYMAP | Property maps but with a more flexible framework for the distance metric being used. | COLVAR |
| GRADIENT | Calculate the gradient of an input grid | MCOLVAR |
| GROUP | Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. | GENERIC |
| GSYMFUNC_THREEBODY | Calculate functions of the coordinates of the coordinates of all pairs of bonds in the first coordination sphere of an atom | COLVAR |
| GYRATION | Calculate the radius of gyration, or other properties related to it. | COLVAR |
| GYRATION_TENSOR | Calculate the gyration tensor using a user specified vector of weights | MCOLVAR |
| HBOND_MATRIX | Adjacency matrix in which two atoms are adjacent if there is a hydrogen bond between them. | MATRIX |
| HBPAMM_MATRIX | Adjacency matrix in which two electronegative atoms are adjacent if they are hydrogen bonded | MATRIX |
| HBPAMM_SA | Calculate the number of hydrogen bonds each acceptor participates in using the HBPamm method | COLVAR |
| HBPAMM_SD | Calculate the number of hydrogen bonds each donor participates in using the HBPamm method | COLVAR |
| HBPAMM_SH | Calculate the number of hydrogen bonds each hydrogen participates in using the HBPamm method | COLVAR |
| HEXACTIC_PARAMETER | Calculate the hexatic order parameter | MCOLVAR |
| HIGHEST | This function can be used to find the highest colvar by magnitude in a set. | FUNCTION |
| HISTOGRAM | Accumulate the average probability density along a few CVs from a trajectory. | GRIDCALC |
| INCLUDE | Includes an external input file, similar to #include in C preprocessor. | GENERIC |
| INCYLINDER | 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. | VOLUMES |
| INENVELOPE | This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a region where the density of a certain type of atom is high. | VOLUMES |
| INPLANEDISTANCES | Calculate distances in the plane perpendicular to an axis | MCOLVAR |
| INSPHERE | 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. | VOLUMES |
| INTEGRATE_GRID | Calculate the numerical integral of the function stored on the grid | GRIDANALYSIS |
| INTERPOLATE_GRID | Interpolate a smooth function stored on a grid onto a grid with a smaller grid spacing. | GRIDANALYSIS |
| INVERT_MATRIX | Calculate the inverse of the input matrix | MCOLVAR |
| JCOUPLING | Calculates 3J coupling constants for a dihedral angle. | ISDB_COLVAR |
| KDE | Create a histogram from the input scalar/vector/matrix using KDE | ANALYSIS |
| KERNEL | Transform a set of input coordinates using a kernel function | FUNCTION |
| KL_ENTROPY | Calculate the KL entropy of a distribution | ANALYSIS |
| LANDMARK_SELECT_FPS | Select a of landmarks from a large set of configurations using farthest point sampling. | LANDMARKS |
| LANDMARK_SELECT_RANDOM | Select a random set of landmarks from a large set of configurations. | LANDMARKS |
| LANDMARK_SELECT_STRIDE | Select every ith frame from the stored set of configurations | LANDMARKS |
| LESS_THAN | Use a switching function to determine how many of the input variables are less than a certain cutoff. | FUNCTION |
| LOAD | Loads a library, possibly defining new actions. | GENERIC |
| LOCALENSEMBLE | Calculates the average over multiple arguments. | FUNCTION |
| LOCAL_AVERAGE | Calculate averages over spherical regions centered on atoms | MCOLVARF |
| LOCAL_CRYSTALINITY | Calculate the local crystalinity symmetry function | MCOLVAR |
| LOCAL_Q1 | Calculate the local degree of order around an atoms by taking the average dot product between the q_1 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere. | MCOLVARF |
| LOCAL_Q3 | 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 vector on the atoms in the first coordination sphere. | MCOLVARF |
| LOCAL_Q4 | 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 vector on the atoms in the first coordination sphere. | MCOLVARF |
| LOCAL_Q6 | 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 vector on the atoms in the first coordination sphere. | MCOLVARF |
| LOGMFD | Used to perform LogMFD, LogPD, and TAMD/d-AFED. | BIAS |
| LOGSUMEXP | This action takes the exponential of a vector of logarithms and divides each element of the vector by the sum of the exponentials. | ANALYSIS |
| LOWER_WALLS | Defines a wall for the value of one or more collective variables, | BIAS |
| LOWEST | This function can be used to find the lowest colvar by magnitude in a set. | FUNCTION |
| MAHALANOBIS_DISTANCE | Calculate the Mahalanobis distance between two points in CV space | FUNCTION |
| MASS | Get the mass of one or multiple atoms | MCOLVAR |
| MATHEVAL | An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. | FUNCTION |
| MATRIX_PRODUCT | Calculate the product of two matrices | MCOLVAR |
| MATRIX_PRODUCT_DIAGONAL | Calculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector | FUNCTION |
| MATRIX_VECTOR_PRODUCT | Calculate the product of the matrix and the vector | MCOLVAR |
| MAXENT | Add a linear biasing potential on one or more variables that satisfies a maximum entropy principle. | BIAS |
| MAZE_LOSS | Define a coarse-grained loss function describing interactions in a | MAZE_LOSS_FUNCTION |
| MAZE_MEMETIC_SAMPLING | Calculates the biasing direction along which the ligand unbinds by | MAZE_OPTIMIZER |
| MAZE_OPTIMIZER_BIAS | Biases the ligand along the direction calculated by the chosen MAZE_OPTIMIZER. | MAZE_BIAS |
| MAZE_RANDOM_ACCELERATION_MD | Performs random acceleration MD within the protein matrix. | MAZE_OPTIMIZER |
| MAZE_RANDOM_WALK | Fake optimizer that can be used for debugging. | MAZE_OPTIMIZER |
| MAZE_SIMULATED_ANNEALING | Calculates the biasing direction along which the ligand unbinds by minimizing | MAZE_OPTIMIZER |
| MAZE_STEERED_MD | Performs a linear unbinding along a predefined biasing direction that | MAZE_OPTIMIZER |
| MEAN | Calculate the arithmetic mean of the elements in a vector | COLVAR |
| MEMFUSIONP | Calculate a CV that can induce the formation of the hemifusion stalk between two initially flat and planar bilayers. | COLVAR |
| METAD | Used to performed metadynamics on one or more collective variables. | BIAS |
| METAINFERENCE | Calculates the Metainference energy for a set of experimental data. | ISDB_BIAS |
| METATOMIC | Use arbitrary machine learning models as collective variables. | COLVAR |
| MFILTER_LESS | Apply a switching function to the input vector. | MCOLVAR |
| MFILTER_MORE | Apply one minus a switching function to the input vector. | MCOLVAR |
| MOLINFO | This command is used to provide information on the molecules that are present in your system. | TOPOLOGY |
| MOMENTS | Calculate central moments from the distribution of input quantities | FUNCTION |
| MORE_THAN | Use a switching function to determine how many of the input variables are more than a certain cutoff. | FUNCTION |
| MOVINGRESTRAINT | Add a time-dependent, harmonic restraint on one or more variables. | BIAS |
| MULTICOLVARDENS | Evaluate the average value of a multicolvar on a grid. | GRIDCALC |
| MULTI_RMSD | Calculate RMSD distances for different domains and combine them. | DCOLVAR |
| NEIGHBORS | Build a matrix with ones in for the N nearest neighbours of an atom | MCOLVAR |
| NOE | Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms | ISDB_COLVAR |
| NORMALIZED_EUCLIDEAN_DISTANCE | Calculate the normalised euclidean distance between two points in CV space | FUNCTION |
| ONES | Create a constant vector with all elements equal to one | COLVAR |
| OPES_EXPANDED | On-the-fly probability enhanced sampling with expanded ensembles for the target distribution. | BIAS |
| OPES_METAD | On-the-fly probability enhanced sampling with metadynamics-like target distribution. | BIAS |
| OPES_METAD_EXPLORE | On-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. | BIAS |
| OPT_ADAM | Adaptive moment estimation (ADAM) optimizer. | VES_OPTIMIZER |
| OPT_AVERAGED_SGD | Averaged stochastic gradient decent with fixed step size. | VES_OPTIMIZER |
| OPT_DUMMY | Dummy optimizer for debugging. | VES_OPTIMIZER |
| OPT_ROBBINS_MONRO_SGD | Robbins-Monro stochastic gradient decent. | VES_OPTIMIZER |
| OUTER_PRODUCT | Calculate the outer product matrix of two vectors | COLVAR |
| OUTPUT_CLUSTER | Output the indices of the atoms in one of the clusters identified by a clustering object | CONCOMP |
| PAIRENTROPIES | Calculate the KL entropy from the RDF around each of the atoms | MCOLVAR |
| PAIRENTROPY | Calculate the KL Entropy from the radial distribution function | MCOLVAR |
| PAMM | Probabilistic analysis of molecular motifs. | MCOLVARF |
| PARABETARMSD | Probe the parallel beta sheet content of your protein structure. | COLVAR |
| PATH | Path collective variables with a more flexible framework for the distance metric being used. | COLVAR |
| PATHMSD | This Colvar calculates path collective variables. | COLVAR |
| PBC | Pass the cell vectors into PLUMED. | ANALYSIS |
| PBMETAD | Used to performed Parallel Bias metadynamics. | BIAS |
| PCA | Perform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input. | DIMRED |
| PCARMSD | Calculate the PCA components for a number of provided eigenvectors and an average structure. | DCOLVAR |
| PCAVARS | Projection on principal component eigenvectors or other high dimensional linear subspace | COLVAR |
| PCS | Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization. | ISDB_COLVAR |
| PDB2CONSTANT | Create a constant value from a PDB input file | COLVAR |
| PIECEWISE | Compute a piece wise straight line through its arguments that passes through a set of ordered control points. | FUNCTION |
| PIV | Calculates the PIV-distance. | COLVAR |
| PLANE | Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. | COLVAR |
| PLANES | Calculate the components of the normals to the planes containing groups of three atoms. | MCOLVAR |
| PLUMED | Embed a separate PLUMED instance. | GENERIC |
| POSITION | Calculate the components of the position of an atom or atoms. | COLVAR |
| PRE | Calculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms . | ISDB_COLVAR |
| Print quantities to a file. | PRINTANALYSIS | |
| PRINT_NDX | Print an ndx file | PRINTANALYSIS |
| PRODUCT | Calculate the product of the input quantities | FUNCTION |
| PROJECTION_ON_AXIS | Calculate a position based on the projection along and extension from a defined axis. | COLVAR |
| PROJECT_POINTS | Find the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input | DIMRED |
| PROPERTYMAP | Calculate generic property maps. | COLVAR |
| PUCKERING | Calculate sugar pseudorotation coordinates. | COLVAR |
| PUT | Pass data into PLUMED | ANALYSIS |
| PYTORCH_MODEL | Load a PyTorch model compiled with TorchScript. | FUNCTION |
| Q1 | Calculate 1st order Steinhardt parameters | MCOLVAR |
| Q3 | Calculate 3rd order Steinhardt parameters. | MCOLVAR |
| Q4 | Calculate fourth order Steinhardt parameters. | MCOLVAR |
| Q6 | Calculate sixth order Steinhardt parameters. | MCOLVAR |
| QUATERNION | Calculate unit quaternions for molecules. | COLVAR |
| QUATERNION_BOND_PRODUCT_MATRIX | Calculate the product between a matrix of quaternions and the bonds connecting molecules | MCOLVAR |
| QUATERNION_PRODUCT_MATRIX | Calculate the outer product matrix from two vectors of quaternions | MCOLVAR |
| RANDOM_EXCHANGES | Set random pattern for exchanges. | GENERIC |
| RDC | Calculates the (Residual) Dipolar Coupling between two atoms. | ISDB_COLVAR |
| RDF | Calculate the radial distribution function | ANALYSIS |
| READ | Read quantities from a colvar file. | GENERIC |
| READMASSCHARGE | Set the masses and charges from an input PDB file. | COLVAR |
| REFERENCE_GRID | Setup a constant grid by either reading values from a file or definining a function in input | GRIDCALC |
| REPARAMETERIZE_PATH | Take an input path with frames that are not equally spaced and make the frames equally spaced | ANALYSIS |
| RESCALE | Scales the value of an another action, being a Collective Variable or a Bias. | ISDB_BIAS |
| RESET_CELL | This action is used to rotate the full cell | GENERIC |
| RESTART | Activate restart. | GENERIC |
| RESTRAINT | Adds harmonic and/or linear restraints on one or more variables. | BIAS |
| REWEIGHT_BIAS | Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored | REWEIGHTING |
| REWEIGHT_METAD | Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. | REWEIGHTING |
| REWEIGHT_TEMP_PRESS | Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. | REWEIGHTING |
| RMSD | Calculate the RMSD with respect to a reference structure. | DCOLVAR |
| ROPS | Calculate the ROPS order parameter | COLVAR |
| S2CM | S2 contact model CV. | COLVAR |
| SANS | Calculates SANS intensity. | ISDB_COLVAR |
| SASA_HASEL | Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. | COLVAR |
| SASA_LCPO | Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. | COLVAR |
| SAXS | Calculates SAXS intensity. | ISDB_COLVAR |
| SECONDARY_STRUCTURE_DRMSD | Calclulate the distance between segments of a protein and a reference structure of interest | MCOLVAR |
| SECONDARY_STRUCTURE_RMSD | Calclulate the distance between segments of a protein and a reference structure of interest | MCOLVAR |
| SELECT | Selects an argument based on the value of a SELECTOR. | ISDB_FUNCTION |
| SELECTOR | Defines a variable (of the type double) inside the PLUMED code that can be used and modified by other actions. | ISDB_GENERIC |
| SELECT_COMPONENTS | Create a new value to hold a subset of the components that are in a vector or matrix | PRINTANALYSIS |
| SELECT_WITH_MASK | Use a mask to select elements of an array | PRINTANALYSIS |
| SHADOW | Communicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation. | ISDB_COLVAR |
| SIMPLECUBIC | Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simple cubic structure. | MCOLVAR |
| SIZESHAPE_POSITION_LINEAR_PROJ | Calculates a linear projection in the space of a given reference configurational distribution in size-and-shape space. | COLVAR |
| SIZESHAPE_POSITION_MAHA_DIST | Calculates Mahalanobis distance of a current configuration from a given reference configurational distribution in size-and-shape space. | COLVAR |
| SKETCHMAP | Construct a sketch map projection of the input data | DIMRED |
| SKETCHMAP_PROJECTION | Read in a sketch-map projection | DIMRED |
| SMAC | Calculate the SMAC order parameter for a set of molecules | MCOLVAR |
| SORT | This function can be used to sort colvars according to their magnitudes. | FUNCTION |
| SPHERICAL_HARMONIC | Calculate the values of all the spherical harmonic funtions for a particular value of l. | MCOLVAR |
| SPHERICAL_KDE | Create a histogram from the input scalar/vector/matrix using SPHERICAL_KDE | ANALYSIS |
| SPRINT | Calculate SPRINT topological variables from an adjacency matrix. | MATRIXF |
| STATS | Calculates statistical properties of a set of collective variables with respect to a set of reference values. | FUNCTION |
| SUM | Calculate the sum of the arguments | COLVAR |
| TD_CHI | Chi distribution (static). | VES_TARGETDIST |
| TD_CHISQUARED | Chi-squared distribution (static). | VES_TARGETDIST |
| TD_CUSTOM | Target distribution given by an arbitrary mathematical expression (static or dynamic). | VES_TARGETDIST |
| TD_EXPONENTIAL | Exponential distribution (static). | VES_TARGETDIST |
| TD_EXPONENTIALLY_MODIFIED_GAUSSIAN | Target distribution given by a sum of exponentially modified Gaussian distributions (static). | VES_TARGETDIST |
| TD_GAUSSIAN | Target distribution given by a sum of Gaussian kernels (static). | VES_TARGETDIST |
| TD_GENERALIZED_EXTREME_VALUE | Generalized extreme value distribution (static). | VES_TARGETDIST |
| TD_GENERALIZED_NORMAL | Target distribution given by a sum of generalized normal distributions (static). | VES_TARGETDIST |
| TD_GRID | Target distribution from an external grid file (static). | VES_TARGETDIST |
| TD_LINEAR_COMBINATION | Target distribution given by linear combination of distributions (static or dynamic). | VES_TARGETDIST |
| TD_MULTICANONICAL | Multicanonical target distribution (dynamic). | VES_TARGETDIST |
| TD_MULTITHERMAL_MULTIBARIC | Multithermal-multibaric target distribution (dynamic). | VES_TARGETDIST |
| TD_PRODUCT_COMBINATION | Target distribution given by product combination of distributions (static or dynamic). | VES_TARGETDIST |
| TD_PRODUCT_DISTRIBUTION | Target distribution given by a separable product of one-dimensional distributions (static or dynamic). | VES_TARGETDIST |
| TD_UNIFORM | Uniform target distribution (static). | VES_TARGETDIST |
| TD_VONMISES | Target distribution given by a sum of Von Mises distributions (static). | VES_TARGETDIST |
| TD_WELLTEMPERED | Well-tempered target distribution (dynamic). | VES_TARGETDIST |
| TEMPLATE | This file provides a template for if you want to introduce a new CV. | COLVAR |
| TETRAHEDRAL | Calculate the degree to which the environment about ions has a tetrahedral order. | MCOLVAR |
| TETRAHEDRALPORE | This quantity can be used to calculate functions of the distribution of collective variables for the atoms lie that lie in a box defined by the positions of four atoms at the corners of a tetrahedron. | VOLUMES |
| TETRA_ANGULAR | Calculate the angular tetra CV | MCOLVAR |
| TETRA_RADIAL | Calculate the radial tetra CV | MCOLVAR |
| TIME | retrieve the time of the simulation to be used elsewhere | GENERIC |
| TOPOLOGY_MATRIX | Adjacency matrix in which two atoms are adjacent if they are connected topologically | MATRIX |
| TORSION | Calculate one or multiple torsional angles. | COLVAR |
| TORSIONS | Calculate whether or not a set of torsional angles are within a particular range. | MCOLVAR |
| TORSIONS_MATRIX | Calculate the matrix of torsions between two vectors of molecules | MCOLVAR |
| TRANSPOSE | Calculate the transpose of a matrix | MCOLVAR |
| UNITS | This command sets the internal units for the code. | GENERIC |
| UPDATE_IF | Conditional update of other actions. | PRINTANALYSIS |
| UPPER_WALLS | Defines a wall for the value of one or more collective variables, | BIAS |
| UWALLS | Add lower walls to a vector of quantities | MCOLVAR |
| VES_DELTA_F | Implementation of VES Delta F method | VES_BIAS |
| VES_LINEAR_EXPANSION | Linear basis set expansion bias. | VES_BIAS |
| VES_OUTPUT_BASISFUNCTIONS | Output basis functions to file. | VES_UTILS |
| VES_OUTPUT_FES | Tool to output biases and free energy surfaces for VES biases from previously obtained coefficients. | VES_UTILS |
| VES_OUTPUT_TARGET_DISTRIBUTION | Output target distribution to file. | VES_UTILS |
| VOLUME | Calculate the volume the simulation box. | COLVAR |
| VORONOI | Do a voronoi analysis | MCOLVAR |
| VSTACK | Create a matrix by stacking vectors together | MCOLVAR |
| WHAM | Calculate the weights for configurations using the weighted histogram analysis method. | REWEIGHTING |
| WHAM_HISTOGRAM | This can be used to output the a histogram using the weighted histogram technique | REWEIGHTING |
| WHAM_WEIGHTS | Calculate and output weights for configurations using the weighted histogram analysis method. | REWEIGHTING |
| WHOLEMOLECULES | This action is used to rebuild molecules that can become split by the periodic boundary conditions. | GENERIC |
| WRAPAROUND | Rebuild periodic boundary conditions around chosen atoms. | GENERIC |
| XANGLES | Calculate the angle between an arbitrary vector and the positive x direction | COLVAR |
| XDISTANCES | Calculate the x components of the vectors connecting one or many pairs of atoms. | MCOLVAR |
| XYTORSIONS | Calculate the torsional angle around the x axis between an arbitrary vector and the positive y direction | COLVAR |
| XZTORSIONS | Calculate the torsional angle around the x axis between an arbitrary vector and the positive z direction | COLVAR |
| YANGLES | Calculate the angle between an arbitrary vector and the positive y direction | COLVAR |
| YDISTANCES | Calculate the y components of the vectors connecting one or many pairs of atoms. | MCOLVAR |
| YXTORSIONS | Calculate the torsional angle around the y axis between an arbitrary vector and the positive x direction | COLVAR |
| YZTORSIONS | Calculate the torsional angle around the y axis between an arbitrary vector and the positive z direction | COLVAR |
| ZANGLES | Calculate the angle between an arbitrary vector and the positive z direction | COLVAR |
| ZDISTANCES | Calculate the z components of the vectors connecting one or many pairs of atoms. | MCOLVAR |
| ZXTORSIONS | Calculate the torsional angle around the z axis between an arbitrary vector and the positive x direction | COLVAR |
| ZYTORSIONS | Calculate the torsional angle around the z axis between an arbitrary vector and the positive y direction | COLVAR |