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:
| ABMD | BIAS | Adds a ratchet-and-pawl like restraint on one or more variables. |
| ADAPTIVE_PATH | COLVAR | Compute path collective variables that adapt to the lowest free energy path connecting states A and B. |
| 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. |
| ANGLE | COLVAR | Calculate an angle. |
| ANGLES | MCOLVAR | Calculate functions of the distribution of angles . |
| ANN | ANNMOD_Function | Calculates the ANN-function. |
| 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 collective variables 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 |
| BF_CHEBYSHEV | VES_BASISF | Chebyshev polynomial basis functions. |
| BF_COMBINED | VES_BASISF | Combining other basis functions types |
| BF_COSINE | VES_BASISF | Fourier cosine basis functions. |
| BF_CUBIC_B_SPLINES | VES_BASISF | Cubic B spline basis functions. |
| BF_CUSTOM | VES_BASISF | Basis functions given by arbitrary mathematical expressions. |
| BF_FOURIER | VES_BASISF | Fourier basis functions. |
| BF_GAUSSIANS | VES_BASISF | Gaussian basis functions. |
| BF_LEGENDRE | VES_BASISF | Legendre polynomials basis functions. |
| BF_POWERS | VES_BASISF | Polynomial power basis functions. |
| BF_SINE | VES_BASISF | Fourier sine basis functions. |
| BF_WAVELETS | VES_BASISF | Daubechies Wavelets basis functions. |
| BIASVALUE | BIAS | Takes the value of one variable and use it as a bias |
| BOND_DIRECTIONS | MCOLVAR | Calculate the vectors connecting atoms that are within cutoff defined using a switching function. |
| BRIDGE | MCOLVAR | Calculate the number of atoms that bridge two parts of a structure |
| CALIBER | ISDB_BIAS | Add a time-dependent, harmonic restraint on one or more variables. |
| CAVITY | VOLUMES | 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. |
| CELL | COLVAR | Calculate the components of the simulation cell |
| CENTER | VATOM | Calculate the center for a group of atoms, with arbitrary weights. |
| CENTER_OF_MULTICOLVAR | VATOM | Calculate a a weighted average position based on the value of some multicolvar. |
| CLASSICAL_MDS | DIMRED | Create a low-dimensional projection of a trajectory using the classical multidimensional scaling 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. |
| COLLECT_FRAMES | ANALYSIS | This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object |
| COLUMNSUMS | MATRIXF | Sum the columns of a contact matrix |
| COM | VATOM | Calculate the center of mass for a group of atoms. |
| COMBINE | FUNCTION | Calculate a polynomial combination of a set of other variables. |
| COMMITTOR | PRINTANALYSIS | Does a committor analysis. |
| CONSTANT | COLVAR | Return one or more constant quantities with or without derivatives. |
| CONTACTMAP | COLVAR | Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. |
| 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). |
| COORDINATION | COLVAR | Calculate coordination numbers. |
| COORDINATIONNUMBER | MCOLVAR | Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of coordination numbers such as the minimum, the number less than a certain quantity and so on. |
| CS2BACKBONE | ISDB_COLVAR | Calculates the backbone chemical shifts for a protein. |
| CUSTOM | FUNCTION | Calculate a combination of variables using a custom expression. |
| 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 calculate the 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. |
| DIMER | COLVAR | This CV computes the dimer interaction energy for a collection of dimers. |
| DIPOLE | COLVAR | Calculate the dipole moment for a group of atoms. |
| DISTANCE | COLVAR | Calculate the distance between a pair of atoms. |
| DISTANCES | MCOLVAR | Calculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of distances such as the minimum, the number less than a certain quantity and so on. |
| DISTANCE_FROM_CONTOUR | COLVAR | Calculate the perpendicular distance from a Willard-Chandler dividing surface. |
| DRMSD | DCOLVAR | Calculate the distance RMSD with respect to a reference structure. |
| DRR | EABFMOD_BIAS | Used to performed extended-system adaptive biasing force(eABF) |
| 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. |
| DUMPGRAPH | CONCOMP | Write out the connectivity of the nodes in the graph in dot format. |
| 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). |
| ECV_CUSTOM | OPES_EXPANSION_CV | Use some given CVs as a set of expansion collective variables (ECVs). |
| ECV_LINEAR | OPES_EXPANSION_CV | Linear expansion, according to a parameter lambda. |
| ECV_MULTITHERMAL | OPES_EXPANSION_CV | Expand a simulation to sample multiple temperatures simultaneously. |
| ECV_MULTITHERMAL_MULTIBARIC | OPES_EXPANSION_CV | Expand a simulation to sample multiple temperatures and pressures. |
| ECV_UMBRELLAS_FILE | OPES_EXPANSION_CV | Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. |
| ECV_UMBRELLAS_LINE | OPES_EXPANSION_CV | Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. |
| EDS | EDSMOD_BIAS | Add a linear bias on a set of observables. |
| EEFSOLV | COLVAR | Calculates EEF1 solvation free energy for a group of atoms. |
| EFFECTIVE_ENERGY_DRIFT | GENERIC | Print the effective energy drift |
| EMMI | ISDB_COLVAR | Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. |
| ENDPLUMED | GENERIC | Terminate plumed input. |
| ENERGY | COLVAR | Calculate the total potential energy of the simulation box. |
| ENSEMBLE | FUNCTION | Calculates the replica averaging of a collective variable over multiple replicas. |
| ENVIRONMENTSIMILARITY | MCOLVAR | Measure how similar the environment around atoms is to that found in some reference crystal structure. |
| ERMSD | COLVAR | Calculate eRMSD with respect to a reference structure. |
| EUCLIDEAN_DISSIMILARITIES | ANALYSIS | Calculate the matrix of dissimilarities between a trajectory of atomic configurations. |
| EXTENDED_LAGRANGIAN | BIAS | Add extended Lagrangian. |
| EXTERNAL | BIAS | Calculate a restraint that is defined on a grid that is read during start up |
| EXTRACV | COLVAR | Allow PLUMED to use collective variables computed in the MD engine. |
| FAKE | COLVAR | This is a fake colvar container used by cltools or various other actions that supports input and period definitions |
| FCCUBIC | MCOLVAR | Measure how similar the environment around atoms is to that found in a FCC structure. |
| FIND_CONTOUR | GRIDANALYSIS | Find an isocontour in a smooth function. |
| FIND_CONTOUR_SURFACE | GRIDANALYSIS | Find an isocontour by searching along either the x, y or z direction. |
| FIND_SPHERICAL_CONTOUR | GRIDANALYSIS | Find an isocontour in a three dimensional grid by searching over a Fibonacci sphere. |
| FISST | FISSTMOD_BIAS | Compute and apply the optimal linear force on an observable to enhance sampling of conformational distributions over a range of applied forces. |
| 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 | ISDB_COLVAR | Calculates the FRET efficiency between a pair of atoms.The efficiency is calculated using the Forster relation: |
| FUNCPATHGENERAL | FUNCTION | This function calculates path collective variables (PCVs) using an arbitrary combination of collective variables. |
| FUNCPATHMSD | FUNCTION | This function calculates path collective variables. |
| FUNCSUMHILLS | FUNCTION | 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!) |
| FUNNEL | FUNNELMOD_BIAS | Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. |
| FUNNEL_PS | FUNNELMOD_COLVAR | FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. |
| FUSIONPOREEXPANSIONP | MEMBRANEFUSIONMOD_COLVAR | A CV for inducing the expansion of a fusion pore from a nucleated fusion pore. |
| FUSIONPORENUCLEATIONP | MEMBRANEFUSIONMOD_COLVAR | A CV for inducing the nucleation of the fusion pore from a hemifusion stalk. |
| GHBFIX | COLVAR | Calculate the GHBFIX interaction energy among GROUPA and GROUPBusing a potential defined in Kührová et al., Improving the performance of the AMBER RNA force field bytuning the hydrogen-bonding interactions, JCTC, 2019. Essentially it is a switching function being -1 for small distances and 0 for large distances with a smooth interpolation in the middle. This can be scaled as desired by specifying interaction scaling parameters and energy units. |
| GHOST | VATOM | Calculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. |
| 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 |
| GRID_TO_XYZ | GRIDANALYSIS | Output the function on the grid to an xyz file |
| GROUP | GENERIC | 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. |
| 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. |
| HBPAMM_MATRIX | MATRIX | Adjacency matrix in which two electronegative atoms are adjacent if they are hydrogen bonded |
| HBPAMM_SH | MCOLVAR | Number of HBPAMM hydrogen bonds formed by each hydrogen atom in the system |
| 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 collective variables for the atoms that lie in a particular, user-specified part of of the cell. |
| INENVELOPE | VOLUMES | 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. |
| 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 collective variables for the atoms that lie in a particular, user-specified part of of the cell. |
| INTEGRATE_GRID | GRIDANALYSIS | Calculate the total integral of the function on the input grid |
| INTERMOLECULARTORSIONS | MCOLVARF | Calculate torsion angles between vectors on adjacent molecules |
| INTERPOLATE_GRID | GRIDANALYSIS | Interpolate a smooth function stored on a grid onto a grid with a smaller grid spacing. |
| JCOUPLING | ISDB_COLVAR | Calculates 3J coupling constants for a dihedral angle. |
| LANDMARK_SELECT_FPS | LANDMARKS | Select a set of landmarks using farthest point sampling. |
| LANDMARK_SELECT_RANDOM | LANDMARKS | Select a random set of landmarks from a large set of configurations. |
| LANDMARK_SELECT_STAGED | LANDMARKS | Select a set of landmarks using the staged algorithm. |
| LANDMARK_SELECT_STRIDE | LANDMARKS | Select every kth landmark from the trajectory. |
| LOAD | GENERIC | Loads a library, possibly defining new actions. |
| LOCALENSEMBLE | FUNCTION | Calculates the average over multiple arguments. |
| 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 vector on 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 vector on 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 vector on the atoms in the first coordination sphere. |
| LOGMFD | LOGMFDMOD_BIAS | Used to perform LogMFD, LogPD, and TAMD/d-AFED. |
| 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. |
| LWALLS | MCOLVARB | Add LOWER_WALLS restraints on all the multicolvar values |
| MATHEVAL | FUNCTION | An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. |
| MAXENT | BIAS | Add a linear biasing potential on one or more variables that satisfies a maximum entropy principle. |
| MAZE_LOSS | MAZE_LOSS | |
| MAZE_MEMETIC_SAMPLING | MAZE_OPTIMIZER | |
| MAZE_OPTIMIZER_BIAS | MAZE_BIAS | |
| MAZE_RANDOM_ACCELERATION_MD | MAZE_OPTIMIZER | |
| MAZE_RANDOM_WALK | MAZE_OPTIMIZER | |
| MAZE_SIMULATED_ANNEALING | MAZE_OPTIMIZER | |
| MAZE_STEERED_MD | MAZE_OPTIMIZER | |
| MCOLV_COMBINE | MCOLVARF | Calculate linear combinations of multiple multicolvars |
| MCOLV_PRODUCT | MCOLVARF | Calculate a product of multiple multicolvars |
| MEMFUSIONP | MEMBRANEFUSIONMOD_COLVAR | Calculate a CV that can induce the formation of the hemifusion stalk between two initially flat and planar bilayers. |
| METAD | BIAS | Used to performed metadynamics on one or more collective variables. |
| METAINFERENCE | ISDB_BIAS | Calculates the Metainference energy for a set of experimental data. |
| MFILTER_BETWEEN | MFILTERS | This action can be used to filter the colvar values calculated by a multicolvar so 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 multicolvar so 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 multicolvar so 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 used to transform the colvar values calculated by a MultiColvar using a histogram bead |
| MTRANSFORM_LESS | MTRANSFORMS | This action can be used to transform the colvar values calculated by a multicovar using a switching function |
| MTRANSFORM_MORE | MTRANSFORMS | This action can be used to transform the colvar values calculated by a multicolvar using one minus a switching function |
| 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 | ISDB_COLVAR | Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms or ambiguous NOE. |
| OPES_EXPANDED | OPES_BIAS | On-the-fly probability enhanced sampling with expanded ensembles for the target distribution. |
| OPES_METAD | OPES_BIAS | On-the-fly probability enhanced sampling with metadynamics-like target distribution. |
| OPES_METAD_EXPLORE | OPES_BIAS | On-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. |
| OPT_ADAM | VES_OPTIMIZER | Adaptive moment estimation (ADAM) optimizer. |
| OPT_AVERAGED_SGD | VES_OPTIMIZER | Averaged stochastic gradient decent with fixed step size. |
| OPT_DUMMY | VES_OPTIMIZER | Dummy optimizer for debugging. |
| OPT_ROBBINS_MONRO_SGD | VES_OPTIMIZER | Robbins-Monro stochastic gradient decent. |
| OUTPUT_ANALYSIS_DATA_TO_COLVAR | ANALYSIS | This can be used to output the data that has been stored in an Analysis object. |
| OUTPUT_ANALYSIS_DATA_TO_PDB | ANALYSIS | This can be used to output the data that has been stored in an Analysis object. |
| OUTPUT_CLUSTER | CONCOMP | Output the indices of the atoms in one of the clusters identified by a clustering object |
| OUTPUT_PCA_PROJECTION | DIMRED | This is used to output the projection calculated by principle component analysis |
| PAMM | MCOLVARF | Probabilistic analysis of molecular motifs. |
| PARABETARMSD | COLVAR | Probe the parallel beta sheet content of your protein structure. |
| PATH | COLVAR | Path collective variables with a more flexible framework for the distance metric being used. |
| PATHMSD | COLVAR | This Colvar calculates path collective variables. |
| PBMETAD | BIAS | Used to performed Parallel Bias metadynamics. |
| PCA | DIMRED | Perform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input. |
| PCARMSD | DCOLVAR | Calculate the PCA components for a number of provided eigenvectors and an average structure. |
| PCAVARS | COLVAR | Projection on principal component eigenvectors or other high dimensional linear subspace |
| PCS | ISDB_COLVAR | Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization. |
| PIECEWISE | FUNCTION | Compute a piece wise straight line through its arguments that passes through a set of ordered control points. |
| PIV | PIVMOD_COLVAR | Calculates the PIV-distance. |
| PLANES | MCOLVAR | Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. |
| PLUMED | GENERIC | Embed a separate PLUMED instance. |
| POLYMER_ANGLES | MCOLVARF | Calculate a function to investigate the relative orientations of polymer angles |
| POSITION | COLVAR | Calculate the components of the position of an atom. |
| PRE | ISDB_COLVAR | Calculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms . |
| PRINT | PRINTANALYSIS | Print quantities to a file. |
| PRINT_DISSIMILARITY_MATRIX | ANALYSIS | Print the matrix of dissimilarities between a trajectory of atomic configurations. |
| PROJECTION_ON_AXIS | COLVAR | Calculate a position based on the projection along and extension from a defined axis. |
| PROJECT_ALL_ANALYSIS_DATA | DIMRED | Find projections of all non-landmark points using the embedding calculated by a dimensionality reduction optimization calculation. |
| PROPERTYMAP | COLVAR | Calculate generic property maps. |
| PUCKERING | COLVAR | Calculate sugar pseudorotation coordinates. |
| PYTORCH_MODEL | PYTORCH_FUNCTION | Load a PyTorch model compiled with TorchScript. |
| Q3 | MCOLVAR | Calculate 3rd order Steinhardt parameters. |
| Q4 | MCOLVAR | Calculate fourth order Steinhardt parameters. |
| Q6 | MCOLVAR | Calculate sixth order Steinhardt parameters. |
| RANDOM_EXCHANGES | GENERIC | Set random pattern for exchanges. |
| RDC | ISDB_COLVAR | Calculates the (Residual) Dipolar Coupling between two atoms. |
| READ | GENERIC | Read quantities from a colvar file. |
| READ_DISSIMILARITY_MATRIX | ANALYSIS | Read a matrix of dissimilarities between a trajectory of atomic configurations from a file. |
| RESCALE | ISDB_BIAS | Scales the value of an another action, being a Collective Variable or a Bias. |
| RESELECT_LANDMARKS | LANDMARKS | This allows us to use one measure in landmark selection and a different measure in dimensionality reduction |
| 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_PRESS | REWEIGHTING | Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. |
| REWEIGHT_WHAM | REWEIGHTING | Calculate the weights for configurations using the weighted histogram analysis method. |
| RMSD | DCOLVAR | Calculate the RMSD with respect to a reference structure. |
| ROWSUMS | MATRIXF | Sum the rows of a adjacency matrix. |
| S2CM | S2CMMOD_COLVAR | S2 contact model CV. |
| SANS | ISDB_COLVAR | Calculates SANS intensity. |
| SASA_HASEL | SASAMOD_COLVAR | Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. |
| SASA_LCPO | SASAMOD_COLVAR | Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. |
| SAXS | ISDB_COLVAR | Calculates SAXS intensity. |
| SELECT | ISDB_FUNCTION | Selects an argument based on the value of a SELECTOR. |
| SELECTOR | ISDB_GENERIC | Defines a variable (of the type double) inside the PLUMED code that can be used and modified by other actions. |
| SIMPLECUBIC | MCOLVAR | Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simple cubic structure. |
| SKETCHMAP_CONJGRAD | DIMRED | Optimize the sketch-map stress function using conjugate gradients. |
| SKETCHMAP_POINTWISE | DIMRED | Optimize the sketch-map stress function using a pointwise global optimization algorithm. |
| SKETCHMAP_READ | DIMRED | Read in a sketch-map projection from an input file |
| SKETCHMAP_SMACOF | DIMRED | Optimize the sketch-map stress function using the SMACOF algorithm. |
| SKETCH_MAP | DIMRED | This can be used to output the data that has been stored in an Analysis object. |
| SMAC | MCOLVARF | Calculate a variant on the SMAC collective variable |
| SMACOF_MDS | DIMRED | Optimize the multidimensional scaling stress function using the SMACOF algorithm. |
| 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. |
| 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. |
| TARGET | DCOLVAR | This function measures the Pythagorean distance from a particular structure measured in the space defined by some set of collective variables. |
| TD_CHI | VES_TARGETDIST | Chi distribution (static). |
| TD_CHISQUARED | VES_TARGETDIST | Chi-squared distribution (static). |
| TD_CUSTOM | VES_TARGETDIST | Target distribution given by an arbitrary mathematical expression (static or dynamic). |
| TD_EXPONENTIAL | VES_TARGETDIST | Exponential distribution (static). |
| TD_EXPONENTIALLY_MODIFIED_GAUSSIAN | VES_TARGETDIST | Target distribution given by a sum of exponentially modified Gaussian distributions (static). |
| TD_GAUSSIAN | VES_TARGETDIST | Target distribution given by a sum of Gaussian kernels (static). |
| TD_GENERALIZED_EXTREME_VALUE | VES_TARGETDIST | Generalized extreme value distribution (static). |
| TD_GENERALIZED_NORMAL | VES_TARGETDIST | Target distribution given by a sum of generalized normal distributions (static). |
| TD_GRID | VES_TARGETDIST | Target distribution from an external grid file (static). |
| TD_LINEAR_COMBINATION | VES_TARGETDIST | Target distribution given by linear combination of distributions (static or dynamic). |
| TD_MULTICANONICAL | VES_TARGETDIST | Multicanonical target distribution (dynamic). |
| TD_MULTITHERMAL_MULTIBARIC | VES_TARGETDIST | Multithermal-multibaric target distribution (dynamic). |
| TD_PRODUCT_COMBINATION | VES_TARGETDIST | Target distribution given by product combination of distributions (static or dynamic). |
| TD_PRODUCT_DISTRIBUTION | VES_TARGETDIST | Target distribution given by a separable product of one-dimensional distributions (static or dynamic). |
| TD_UNIFORM | VES_TARGETDIST | Uniform target distribution (static). |
| TD_VONMISES | VES_TARGETDIST | Target distribution given by a sum of Von Mises distributions (static). |
| TD_WELLTEMPERED | VES_TARGETDIST | Well-tempered target distribution (dynamic). |
| TEMPLATE | COLVAR | This file provides a template for if you want to introduce a new CV. |
| TETRAHEDRAL | MCOLVAR | Calculate the degree to which the environment about ions has a tetrahedral order. |
| TETRAHEDRALPORE | VOLUMES | 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. |
| TIME | GENERIC | retrieve the time of the simulation to be used elsewhere |
| TOPOLOGY_MATRIX | MATRIX | Adjacency matrix in which two atoms are adjacent if they are connected topologically |
| TORSION | COLVAR | Calculate a torsional angle. |
| TORSIONS | MCOLVAR | Calculate whether or not a set of torsional angles are within a particular range. |
| UNITS | GENERIC | This command sets the internal units for the code. |
| 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_WALL restraints on all the multicolvar values |
| VES_DELTA_F | VES_BIAS | Implementation of VES Delta F method |
| VES_LINEAR_EXPANSION | VES_BIAS | Linear basis set expansion bias. |
| VES_OUTPUT_BASISFUNCTIONS | VES_UTILS | Output basis functions to file. |
| VES_OUTPUT_FES | VES_UTILS | Tool to output biases and free energy surfaces for VES biases from previously obtained coefficients. |
| VES_OUTPUT_TARGET_DISTRIBUTION | VES_UTILS | Output target distribution to file. |
| VOLUME | COLVAR | Calculate the volume of the simulation box. |
| WHAM_HISTOGRAM | REWEIGHTING | This can be used to output the a histogram using the weighted histogram technique |
| WHAM_WEIGHTS | REWEIGHTING | Calculate and output weights for configurations using the weighted histogram analysis method. |
| WHOLEMOLECULES | GENERIC | This action is used to rebuild molecules that can become split by the periodic boundary conditions. |
| WRAPAROUND | GENERIC | Rebuild periodic boundary conditions around chosen atoms. |
| XANGLES | MCOLVAR | Calculate the angles between the vector connecting two atoms and the x axis. |
| XDISTANCES | MCOLVAR | Calculate the x components of the vectors connecting one or many pairs of atoms.You can then calculate functions of the distribution of values 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. |
| XYTORSIONS | MCOLVAR | Calculate the torsional angle around the x axis from the positive y direction. |
| XZDISTANCES | MCOLVAR | Calculate distance between a pair of atoms neglecting the y-component. |
| XZTORSIONS | MCOLVAR | Calculate the torsional angle around the x axis from the positive z direction. |
| YANGLES | MCOLVAR | Calculate the angles between the vector connecting two atoms and the y axis. |
| YDISTANCES | MCOLVAR | Calculate the y components of the vectors connecting one or many pairs of atoms.You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on. |
| YXTORSIONS | MCOLVAR | Calculate the torsional angle around the y axis from the positive x direction. |
| YZDISTANCES | MCOLVAR | Calculate distance between a pair of atoms neglecting the x-component. |
| YZTORSIONS | MCOLVAR | Calculate the torsional angle around the y axis from the positive z direction. |
| ZANGLES | MCOLVAR | Calculate the angles between the vector connecting two atoms and the z axis. |
| ZDISTANCES | MCOLVAR | Calculate the z components of the vectors connecting one or many pairs of atoms.You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on. |
| ZXTORSIONS | MCOLVAR | Calculate the torsional angle around the z axis from the positive x direction. |
| ZYTORSIONS | MCOLVAR | Calculate the torsional angle around the z axis from the positive y direction. |
| completion | TOOLS | Dumps the body of a bash function to be used for auto completion. |
| config | TOOLS | inquire plumed about how it was configure |
| driver | TOOLS | driver is a tool that allows one to to use plumed to post-process an existing trajectory. |
| driver-float | TOOLS | Equivalent to driver, but using single precision reals. |
| drr_tool | EABFMOD_TOOLS | - Extract .grad and .count files from the binary output .drrstate - Merge windows |
| gen_example | TOOLS | gen_example is a tool that you can use to construct an example for the manual that users can interact with to understand |
| gen_json | TOOLS | gen_json constructs a json file that includes a dictionary of actions, the keywords for those actions and the components and outputs this to standard output |
| gentemplate | TOOLS | gentemplate is a tool that you can use to construct template inputs for the various actions |
| info | TOOLS | This tool allows you to obtain information about your plumed version |
| kt | TOOLS | Print out the value of k_B T at a particular temperature |
| manual | TOOLS | manual is a tool that you can use to construct the manual page fora particular action |
| mklib | TOOLS | compile a .cpp file into a shared library |
| newcv | TOOLS | create a new collective variable from a template |
| partial_tempering | TOOLS | scale parameters in a gromacs topology to implement solute or partial tempering |
| patch | TOOLS | patch an MD engine |
| pathtools | TOOLS | pathtools can be used to construct paths from pdb data |
| pdbrenumber | TOOLS | Modify atom numbers in a PDB, possibly using hybrid-36 coding. |
| pesmd | TOOLS | Pesmd allows one to do (biased) Langevin dynamics on a two-dimensional potential energy surface. |
| selector | TOOLS | create lists of serial atom numbers |
| simplemd | TOOLS | simplemd allows one to do molecular dynamics on systems of Lennard-Jones atoms. |
| sum_hills | TOOLS | sum_hills is a tool that allows one to to use plumed to post-process an existing hills/colvar file |
| ves_md_linearexpansion | VES_TOOLS | Simple MD code for dynamics on a potential energy surface given by a linear basis set expansion. |
| vim2html | TOOLS | convert plumed input file to colored html using vim syntax |
1.8.17