Actions implemented in PLUMED

The actions that can be used within a PLUMED input file are listed below.

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