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. |
| ACCUMULATE | GRIDCALC | Sum the elements of this value over the course of the trajectory |
| ADAPTIVE_PATH | COLVAR | Compute path collective variables that adapt to the lowest free energy path connecting states A and B. |
| ALPHABETA | MCOLVAR | Calculate the alpha beta CV |
| ALPHARMSD | COLVAR | Probe the alpha helical content of a protein structure. |
| ANGLE | COLVAR | Calculate an angle. |
| ANGLES | COLVAR | Calculate an angle. |
| ANGLE_SCALAR | COLVAR | Calculate an angle. |
| ANGLE_VECTOR | COLVAR | Calculate multiple angles. |
| ANN | ANNMOD_Function | Calculates the ANN-function. |
| ANTIBETARMSD | COLVAR | Probe the antiparallel beta sheet content of your protein structure. |
| ARGS2VATOM | VATOM | Create a virtual atom from the input scalars |
| 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. |
| AROUND_CALC | MCOLVAR | Calculate a vector from the input positions with elements equal to one when the positions are in a particular part of the cell and elements equal to zero otherwise |
| ARRANGE_POINTS | DIMRED | 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. |
| ATOMIC_SMAC | MCOLVAR | Calculate the atomic smac CV |
| AVERAGE | GRIDCALC | Calculate the ensemble average of a collective variable |
| AVERAGE_PATH_DISPLACEMENT | ANALYSIS | Accumulate the distances between the reference frames in the paths and the configurations visited |
| BAIES | ISDB_COLVAR | Bayesian refinement of AF models. |
| BESSEL | FUNCTION | Calculate the value of a Bessel function. |
| BESSEL_SCALAR | FUNCTION | Calculate the value of a Bessel function. |
| BESSEL_VECTOR | FUNCTION | Calculate the bessel function for all the elements in a vector |
| BETWEEN | FUNCTION | Use a switching function to determine how many of the input variables are within a certain range. |
| BETWEEN_MATRIX | COLVAR | Transform all the elements of a matrix using a switching function that is oen when the input value is within a particular range |
| BETWEEN_VECTOR | FUNCTION | Use a switching function to determine how many of the input components are within a certain range |
| 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 |
| BOPS | COLVAR | Calculate the BOPS order parameter |
| BRIDGE | MCOLVAR | Calculate a matrix with elements equal to one if there is a bridging atom between the two atoms |
| BRIDGE_MATRIX | 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. |
| CAVITY_CALC | MCOLVAR | Calculate a vector from the input positions with elements equal to one when the positions are in a particular part of the cell and elements equal to zero otherwise |
| CELL | COLVAR | Calculate the components of the simulation cell |
| CENTER | VATOM | Calculate the center for a group of atoms, with arbitrary weights. |
| CENTER_FAST | VATOM | Calculate the center for a group of atoms, with arbitrary weights. |
| CHARGE | MCOLVAR | Get the charges of one or multiple atoms |
| CHARGE_SCALAR | MCOLVAR | Get the charges of one or multiple atoms |
| CHARGE_VECTOR | MCOLVAR | Get the charges of one or multiple atoms |
| 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_DISTRIBUTION_CALC | CONCOMP | Calculate functions of the distribution of properties in your connected components. |
| CLUSTER_NATOMS | CONCOMP | Calculate the number of atoms in the cluster of interest |
| CLUSTER_PROPERTIES | CONCOMP | Calculate properties of the distribution of some quantities that are part of a connected component |
| CLUSTER_WEIGHTS | CONCOMP | 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. |
| CLUSTER_WITHSURFACE | CONCOMP | Determine the atoms that are within a certain cutoff of the atoms in a cluster |
| COLLECT | ANALYSIS | Collect data from the trajectory for later analysis |
| COLLECT_FRAMES | ANALYSIS | This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object |
| COM | VATOM | Calculate the center of mass for a group of atoms. |
| COMBINE | FUNCTION | Calculate a polynomial combination of a set of other variables. |
| COMBINE_MATRIX | COLVAR | Calculate the sum of a number of matrices |
| COMBINE_SCALAR | FUNCTION | Calculate a polynomial combination of a set of other variables. |
| COMBINE_VECTOR | FUNCTION | Add together the elements of a set of vectors elementwise |
| COMMITTOR | PRINTANALYSIS | Does a committor analysis. |
| CONCATENATE | MCOLVAR | Join vectors or matrices together |
| CONSTANT | COLVAR | Create a constant value that can be passed to actions |
| 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. |
| CONTACT_MATRIX_PROPER | MATRIX | Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. |
| CONVERT_TO_FES | GRIDANALYSIS | Convert a histogram to a free energy surface. |
| 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. |
| COORDINATION_MOMENTS | MCOLVAR | Calculate moments of the distribution of distances in the first coordination sphere |
| COORDINATION_SHELL_AVERAGE | MCOLVAR | Calculate an arbitrary function of all the bond vectors in the first coordination sphere of an atom and take an average |
| COORDINATION_SHELL_FUNCTION | MCOLVAR | Calculate an arbitrary function of all the bond vectors in the first coordination sphere of an atom |
| COORD_ANGLES | MCOLVAR | Calculate all the angles between bonds in the first coordination spheres of a set of atoms |
| COVARIANCE_MATRIX | REWEIGHTING | Calculate a covariance matix |
| CREATE_MASK | DIMRED | Create a mask vector to use for landmark selection |
| CS2BACKBONE | ISDB_COLVAR | Calculates the backbone chemical shifts for a protein. |
| CUSTOM | FUNCTION | Calculate a combination of variables using a custom expression. |
| CUSTOM_GRID | GRIDCALC | Calculate a function of the grid or grids that are input and return a new grid |
| CUSTOM_MATRIX | COLVAR | Calculate an arbitrary function piecewise for one or multiple input matrices. |
| CUSTOM_SCALAR | FUNCTION | Calculate a function of a set of input scalars |
| CUSTOM_VECTOR | FUNCTION | Calculate a function of a set of input vectors elementwise |
| CYLINDRICAL_HARMONIC | MCOLVAR | Calculate the cylindrical harmonic function |
| CYLINDRICAL_HARMONIC_MATRIX | MCOLVAR | Calculate the cylindrical harmonic function from the elements in two input matrices |
| DEBUG | GENERIC | Set some debug options. |
| DENSITY | MCOLVAR | Depreciated command that is bascially equivalant to GROUP. |
| DETERMINANT | MCOLVAR | Calculate the determinant of a matrix |
| 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. |
| DIAGONALIZE | ANALYSIS | Calculate the eigenvalues and eigenvectors of a square matrix |
| DIFFERENCE | FUNCTION | Calculate the differences between two scalars |
| DIFFERENCE_SCALAR | FUNCTION | Calculate the differences between two scalars |
| DIFFERENCE_VECTOR | FUNCTION | Calculate the differences between the elements of two vectors |
| DIHCOR | COLVAR | Measures the degree of similarity between dihedral angles. |
| DIHEDRAL_CORRELATION | COLVAR | Measure the correlation between a pair of dihedral angles |
| DIHEDRAL_CORRELATION_SCALAR | COLVAR | Measure the correlation between a multiple pairs of dihedral angles |
| DIHEDRAL_CORRELATION_VECTOR | COLVAR | Measure the correlation between a multiple pairs of 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. |
| DIPOLE_SCALAR | COLVAR | Calculate the dipole moment for a group of atoms. |
| DIPOLE_VECTOR | MCOLVAR | Calculate a vector of dipole moments for a set of groups of atoms. |
| DISPLACEMENT | MCOLVAR | Calculate the displacement vector between the pair of input vectors |
| DISSIMILARITIES | ANALYSIS | Calculate the matrix of dissimilarities between a trajectory of atomic configurations. |
| DISTANCE | COLVAR | Calculate the distance between a pair of atoms. |
| DISTANCES | MCOLVAR | Calculate the distances between multiple piars of atoms |
| DISTANCE_FROM_CONTOUR | COLVAR | Calculate the perpendicular distance from a Willard-Chandler dividing surface. |
| DISTANCE_FROM_SPHERICAL_CONTOUR | COLVAR | Calculate the perpendicular distance from a Willard-Chandler dividing surface. |
| DISTANCE_MATRIX | MATRIX | Calculate a matrix of distances |
| DISTANCE_SCALAR | MCOLVAR | Calculate the distance between a pair of atoms |
| DISTANCE_VECTOR | MCOLVAR | Calculate a vector containing the distances between various pairs of atoms |
| DOMAIN_DECOMPOSITION | ANALYSIS | Pass domain decomposed properties of atoms to PLUMED |
| DOPS | COLVAR | Calculate the DOPS order parameter |
| 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. |
| DUMPCONTOUR | GRIDANALYSIS | Print the contour |
| 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 | MCOLVAR | Basically equivalent to DUMPATOMS |
| DUMPPDB | PRINTANALYSIS | Output PDB file. |
| DUMPPROJECTIONS | PRINTANALYSIS | Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). |
| DUMPVECTOR | PRINTANALYSIS | Print a vector to a file |
| 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. |
| EMMIVOX | ISDB_COLVAR | Bayesian single-structure and ensemble refinement with cryo-EM maps. |
| 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_DISTANCE | MCOLVAR | Calculate the euclidean distance between two vectors of arguments |
| EVALUATE_FUNCTION_FROM_GRID | GRIDCALC | Calculate the function stored on the input grid at an arbitrary point |
| EVALUATE_FUNCTION_FROM_GRID_SCALAR | GRIDCALC | Calculate the function stored on the input grid at an arbitrary point |
| EVALUATE_FUNCTION_FROM_GRID_VECTOR | GRIDCALC | Calculate the function stored on the input grid for each of the points in the input vector/s |
| 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 |
| FARTHEST_POINT_SAMPLING | LANDMARKS | Select a set of landmarks using farthest point sampling. |
| FCCUBIC | MCOLVAR | Measure how similar the environment around atoms is to that found in a FCC structure. |
| FCCUBIC_FUNC | MCOLVAR | Measure how similar the environment around atoms is to that found in a FCC structure. |
| FCCUBIC_FUNC_MATRIX | 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_GRID_MAXIMUM | GRIDCALC | Find the point with the highest value of the function on the grid |
| FIND_GRID_MINIMUM | GRIDCALC | Find the point with the lowest value of the function on the grid |
| 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. |
| FLATTEN | FUNCTION | Convert a matrix into a vector |
| 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. |
| GATHER_REPLICAS | ANALYSIS | Create a vector that contains the copies of the input quantities from all replicas |
| GEOMETRIC_PATH | COLVAR | Distance along and from a path calculated using geometric formulas |
| GET | ANALYSIS | Get data from PLUMED for another code |
| 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. |
| GPATH | COLVAR | Distance along and from a path calculated using geometric formulas |
| GPROPERTYMAP | COLVAR | Property maps but with a more flexible framework for the distance metric being used. |
| GRADIENT | MCOLVAR | Calculate the gradient of an input grid |
| 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. |
| GSYMFUNC_THREEBODY | COLVAR | Calculate functions of the coordinates of the coordinates of all pairs of bonds in the first coordination sphere of an atom |
| GYRATION | COLVAR | Calculate the radius of gyration, or other properties related to it. |
| GYRATION_FAST | COLVAR | Calculate the radius of gyration, or other properties related to it. |
| GYRATION_TENSOR | MCOLVAR | Calculate the gyration tensor using a user specified vector of weights |
| 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_SA | COLVAR | Calculate the number of hydrogen bonds each acceptor participates in using the HBPamm method |
| HBPAMM_SD | COLVAR | Calculate the number of hydrogen bonds each donor participates in using the HBPamm method |
| HBPAMM_SH | COLVAR | Calculate the number of hydrogen bonds each hydrogen participates in using the HBPamm method |
| HEXACTIC_PARAMETER | MCOLVAR | Calculate the hexatic order parameter |
| HIGHEST | FUNCTION | This function can be used to find the highest colvar by magnitude in a set. |
| HIGHEST_SCALAR | COLVAR | Calculate the highest of a set of sclalar arguments |
| HIGHEST_VECTOR | COLVAR | Calculate the largest element in a vector of inputs |
| 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. |
| INCYLINDER_CALC | MCOLVAR | Calculate a vector from the input positions with elements equal to one when the positions are in a particular part of the cell and elements equal to zero otherwise |
| 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. |
| INENVELOPE_CALC | 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 the distance between a pair of atoms in the plane |
| 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. |
| INSPHERE_CALC | MCOLVAR | Calculate a vector from the input positions with elements equal to one when the positions are in a particular part of the cell and elements equal to zero otherwise |
| INTEGRATE_GRID | GRIDCALC | Calculate the numerical integral of the function stored on the grid |
| INTERPOLATE_GRID | GRIDANALYSIS | Interpolate a smooth function stored on a grid onto a grid with a smaller grid spacing. |
| INVERT_MATRIX | MCOLVAR | Calculate the inverse of the input matrix |
| JCOUPLING | ISDB_COLVAR | Calculates 3J coupling constants for a dihedral angle. |
| KDE | ANALYSIS | Create a histogram from the input scalar/vector/matrix using KDE |
| KERNEL | FUNCTION | Use a switching function to determine how many of the input variables are less than a certain cutoff. |
| KL_ENTROPY | ANALYSIS | Calculate the KL entropy of a distribution |
| LANDMARK_SELECT_FPS | LANDMARKS | Select a of landmarks from a large set of configurations using farthest point sampling. |
| LANDMARK_SELECT_RANDOM | LANDMARKS | Select a random set of landmarks from a large set of configurations. |
| LANDMARK_SELECT_STRIDE | LANDMARKS | Select every ith frame from the stored data |
| LESS_THAN | FUNCTION | Use a switching function to determine how many of the input variables are less than a certain cutoff. |
| LESS_THAN_MATRIX | COLVAR | Transform all the elements of a matrix using a switching function that is one when the input value is smaller than a threshold |
| LESS_THAN_VECTOR | FUNCTION | Use a switching function to determine how many components of the vector are less than a certain cutoff. |
| 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_CRYSTALINITY | MCOLVAR | Calculate the local crystalinity symmetry function |
| LOCAL_Q1 | MCOLVARF | 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. |
| 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. |
| LOGSUMEXP | ANALYSIS | This action takes the exponential of a vector of logarithms and divides each element of the vector by the sum of the exponentials. |
| 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. |
| LOWER_WALLS_SCALAR | 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. |
| LOWEST | FUNCTION | This function can be used to find the lowest colvar by magnitude in a set. |
| LOWEST_SCALAR | COLVAR | Calculate the lowest of a set of sclalar arguments |
| LOWEST_VECTOR | COLVAR | Calculate the lowest element in a vector of inputs |
| MAHALANOBIS_DISTANCE | FUNCTION | Calculate the mahalanobis distance between two points in CV space |
| MASS | MCOLVAR | Get the mass of one or multiple atoms |
| MASS_SCALAR | MCOLVAR | Get the mass of one or multiple atoms |
| MASS_VECTOR | MCOLVAR | Get the mass of one or multiple atoms |
| MATHEVAL | FUNCTION | An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. |
| MATHEVAL_GRID | GRIDCALC | Calculate a function of the grid or grids that are input and return a new grid |
| MATHEVAL_MATRIX | COLVAR | Calculate an arbitrary function piecewise for one or multiple input matrices. |
| MATHEVAL_SCALAR | FUNCTION | Calculate a function of a set of input scalars |
| MATHEVAL_VECTOR | FUNCTION | Calculate a function of a set of input vectors elementwise |
| MATRIX_PRODUCT | MCOLVAR | Calculate the product of two matrices |
| MATRIX_PRODUCT_DIAGONAL | FUNCTION | Calculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector |
| MATRIX_VECTOR_PRODUCT | MCOLVAR | Calculate the product of the matrix and the vector |
| 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 | |
| MEAN | COLVAR | Calculate the arithmetic mean of the elements in a vector |
| MEAN_SCALAR | COLVAR | Calculate the arithmetic mean of the set of input scalars |
| MEAN_VECTOR | COLVAR | Calculate the arithmetic mean of the elements in a vector |
| 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. |
| METATOMIC | METATOMICMOD_COLVAR | Use arbitrary machine learning models as collective variables. |
| MFILTER_LESS | MCOLVAR | Basically equivalent to LESS_THAN. |
| MFILTER_MORE | MCOLVAR | Basically equivalent to MORE_THAN. |
| MOLINFO | TOPOLOGY | This command is used to provide information on the molecules that are present in your system. |
| MOMENTS | FUNCTION | Calculate the moments of the distribution of input quantities |
| MOMENTS_SCALAR | FUNCTION | Calculate the moments of the distribution of input quantities |
| MOMENTS_VECTOR | FUNCTION | Calculate the moments of the distribution of input vectors |
| MORE_THAN | FUNCTION | Use a switching function to determine how many of the input variables are more than a certain cutoff. |
| MORE_THAN_MATRIX | COLVAR | Transform all the elements of a matrix using a switching function that is one when the input value is larger than a threshold |
| MORE_THAN_VECTOR | FUNCTION | Use a switching function to determine how many of elements in the input vector are more than a certain cutoff. |
| MOVINGRESTRAINT | BIAS | Add a time-dependent, harmonic restraint on one or more variables. |
| MULTICOLVARDENS | GRIDCALC | Evaluate the average value of a multicolvar on a grid. |
| MULTI_RMSD | DCOLVAR | Calculate RMSD distances for different domains and combine them. |
| NEIGHBORS | MCOLVAR | Build a matrix with ones in for the N nearest neighbours of an atom |
| NOE | ISDB_COLVAR | Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms or ambiguous NOE. |
| NORMALIZED_EUCLIDEAN_DISTANCE | FUNCTION | Calculate the normalised euclidean distance between two points in CV space |
| ONES | COLVAR | Create a constant vector with all elements equal to one |
| 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. |
| OUTER_PRODUCT | COLVAR | Calculate the outer product matrix of two vectors |
| OUTPUT_CLUSTER | CONCOMP | Output the indices of the atoms in one of the clusters identified by a clustering object |
| PAIRENTROPIES | MCOLVAR | Calculate the KL entropy from the RDF around each of the atoms |
| PAIRENTROPY | MCOLVAR | Calculate the KL Entropy from the radial distribution function |
| 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. |
| PBC | ANALYSIS | Pass the cell vectors into PLUMED. |
| 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. |
| PDB2CONSTANT | COLVAR | Create a constant value from a PDB input file |
| PIECEWISE | FUNCTION | Compute a piece wise straight line through its arguments that passes through a set of ordered control points. |
| PIECEWISE_SCALAR | 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. |
| PLANE | COLVAR | Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. |
| PLANES | MCOLVAR | Calculate the components of the normal to the plane containing three atoms |
| PLANE_SCALAR | COLVAR | Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. |
| PLANE_VECTOR | COLVAR | Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule multiple times. |
| PLUMED | GENERIC | Embed a separate PLUMED instance. |
| POSITION | COLVAR | Calculate the components of the position of an atom. |
| POSITION_SCALAR | COLVAR | Calculate the components of the position of an atom. |
| POSITION_VECTOR | COLVAR | Create a vector that holds the components of the position of a set of atoms. |
| 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_NDX | PRINTANALYSIS | Print an ndx file |
| PRODUCT | FUNCTION | Calculate the product of the input quantities |
| PROJECTION_ON_AXIS | COLVAR | Calculate a position based on the projection along and extension from a defined axis. |
| PROJECT_POINTS | DIMRED | 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 |
| PROPERTYMAP | COLVAR | Calculate generic property maps. |
| PUCKERING | COLVAR | Calculate sugar pseudorotation coordinates. |
| PUT | ANALYSIS | Pass data into PLUMED |
| PYTORCH_MODEL | PYTORCH_FUNCTION | Load a PyTorch model compiled with TorchScript. |
| Q1 | MCOLVAR | Calculate 1st order Steinhardt parameters |
| Q3 | MCOLVAR | Calculate 3rd order Steinhardt parameters. |
| Q4 | MCOLVAR | Calculate fourth order Steinhardt parameters. |
| Q6 | MCOLVAR | Calculate sixth order Steinhardt parameters. |
| QUATERNION | COLVAR | Calculate quaternions for molecules. |
| QUATERNION_BOND_PRODUCT_MATRIX | MCOLVAR | Calculate the product between a matrix of quaternions and the bonds |
| QUATERNION_PRODUCT_MATRIX | MCOLVAR | Calculate the outer product matrix from two vectors of quaternions |
| QUATERNION_SCALAR | COLVAR | Calculate a single quaternion |
| QUATERNION_VECTOR | COLVAR | Calculate multiple quaternions |
| RANDOM_EXCHANGES | GENERIC | Set random pattern for exchanges. |
| RDC | ISDB_COLVAR | Calculates the (Residual) Dipolar Coupling between two atoms. |
| RDF | ANALYSIS | Calculate the radial distribution function |
| READ | GENERIC | Read quantities from a colvar file. |
| READMASSCHARGE | COLVAR | Set the masses and charges from an input PDB file. |
| REFERENCE_GRID | GRIDCALC | Setup a constant grid by either reading values from a file or definining a function in input |
| REPARAMETERIZE_PATH | ANALYSIS | Take an input path with frames that are not equally spaced and make the frames equally spaced |
| RESCALE | ISDB_BIAS | Scales the value of an another action, being a Collective Variable or a Bias. |
| 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. |
| RESTRAINT_SCALAR | BIAS | Adds harmonic and/or linear restraints on one or more scalar 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. |
| RMSD | DCOLVAR | Calculate the RMSD with respect to a reference structure. |
| RMSD_SCALAR | DCOLVAR | Calculate the RMSD with respect to a reference structure. |
| RMSD_VECTOR | DCOLVAR | Calculate the RMSD distance between the instaneous configuration and multiple reference configurations |
| ROPS | COLVAR | Calculate the ROPS order parameter |
| 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. |
| SECONDARY_STRUCTURE_RMSD | MCOLVAR | Calclulate the distance between segments of a protein and a reference structure of interest |
| 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. |
| SELECT_COMPONENTS | PRINTANALYSIS | Create a new value to hold a subset of the components that are in a vector or matrix |
| SELECT_WITH_MASK | PRINTANALYSIS | Use a mask to select elements of an array |
| SHADOW | ISDB_COLVAR | Communicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation. |
| SIMPLECUBIC | MCOLVAR | Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simple cubic structure. |
| SIZESHAPE_POSITION_LINEAR_PROJ | sizeshapeMOD_COLVAR | Calculates a linear projection in the space of a given reference configurational distribution in size-and-shape space. |
| SIZESHAPE_POSITION_MAHA_DIST | sizeshapeMOD_COLVAR | Calculates Mahalanobis distance of a current configuration from a given reference configurational distribution in size-and-shape space. |
| SKETCHMAP | DIMRED | Construct a sketch map projection of the input data |
| SKETCHMAP_PROJECTION | DIMRED | Read in a sketch-map projection |
| SMAC | MCOLVAR | Calculate the SMAC order parameter for a set of molecules |
| SORT | FUNCTION | This function can be used to sort colvars according to their magnitudes. |
| SORT_SCALAR | FUNCTION | Sort the input scalars in a vector according to their magnitudes |
| SORT_VECTOR | FUNCTION | Sort the elements in a vector according to their magnitudes |
| SPHERICAL_HARMONIC | MCOLVAR | Calculate the values of all the spherical harmonic funtions for a particular value of l. |
| SPHERICAL_HARMONIC_MATRIX | MCOLVAR | Calculate the values of all the spherical harmonic funtions for a particular value of l for all the elements of a set of three input matrices |
| SPHERICAL_KDE | ANALYSIS | Create a histogram from the input scalar/vector/matrix using SPHERICAL_KDE |
| 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. |
| SUM | COLVAR | Calculate the sum of the arguments |
| SUM_GRID | GRIDCALC | Sum the values of all the function at the points on a grid |
| SUM_MATRIX | COLVAR | Sum all the elements in a matrix |
| SUM_SCALAR | COLVAR | Calculate the SUM of the set of input scalars |
| SUM_VECTOR | COLVAR | Calculate the sum of the elements in a vector |
| 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. |
| TETRAHEDRALPORE_CALC | MCOLVAR | Calculate a vector from the input positions with elements equal to one when the positions are in a particular part of the cell and elements equal to zero otherwise |
| TETRA_ANGULAR | MCOLVAR | Calculate the angular tetra CV |
| TETRA_RADIAL | MCOLVAR | Calculate the radial tetra CV |
| 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. |
| TORSIONS_MATRIX | MCOLVAR | Calculate the matrix of torsions between two vectors of molecules |
| TORSION_SCALAR | COLVAR | Calculate a torsional angle. |
| TORSION_VECTOR | MCOLVAR | Calculate multiple torsional angles. |
| TRANSPOSE | MCOLVAR | Calculate the transpose of a matrix |
| 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. |
| UPPER_WALLS_SCALAR | 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 | MCOLVAR | Add lower walls to a vector of quantities |
| 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. |
| VORONOI | MCOLVAR | Do a voronoi analysis |
| VSTACK | MCOLVAR | Create a matrix by stacking vectors together |
| WHAM | REWEIGHTING | Calculate the weights for configurations using the weighted histogram analysis method. |
| 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 | COLVAR | Calculate the angle between an arbitrary vector and the positive x direction |
| 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. |
| XYTORSIONS | COLVAR | Calculate the torsional angle around the x axis between an arbitrary vector and the positive y direction |
| XZTORSIONS | COLVAR | Calculate the torsional angle around the x axis between an arbitrary vector and the positive z direction |
| YANGLES | COLVAR | Calculate the angle between an arbitrary vector and the positive y direction |
| 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 | COLVAR | Calculate the torsional angle around the y axis between an arbitrary vector and the positive x direction |
| YZTORSIONS | COLVAR | Calculate the torsional angle around the y axis between an arbitrary vector and the positive z direction |
| ZANGLES | COLVAR | Calculate the angle between an arbitrary vector and the positive z direction |
| 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 | COLVAR | Calculate the torsional angle around the z axis between an arbitrary vector and the positive x direction |
| ZYTORSIONS | COLVAR | Calculate the torsional angle around the z axis between an arbitrary vector and the positive y direction |
| benchmark | TOOLS | benchmark is a lightweight reimplementation of driver focused on running benchmarks |
| 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 one or more *.cpp files into a shared libraryERROR: Unknown option –description. Use –help for help. |
| 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. |
| plotswitch | TOOLS | plotswitch is a tool that takes a the input of a switching function and tabulates the output on the terminal |
| selector | TOOLS | create lists of serial atom numbers |
| show_graph | TOOLS | show_graph is a tool that takes a plumed input and generates a graph showing howdata flows through the action set involved. |
| 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 |
1.13.2