| 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 . |
| ANTIBETARMSD | COLVAR | Probe the antiparallel beta sheet content of your protein structure. |
| AROUND | VOLUMES | This quantity can be used to calculate functions of the distribution of collectivevariables for the atoms that lie in a particular, user-specified part of of the cell. |
| AVERAGE | GRIDCALC | Calculate the ensemble average of a collective variable |
| 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_CUSTOM | VES_BASISF | Basis functions given by arbitrary mathematical expressions. |
| BF_FOURIER | VES_BASISF | Fourier 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. |
| 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 |
| CAVITY | VOLUMES | This quantity can be used to calculate functions of the distribution of collectivevariables for the atoms that lie in a box defined by the positions of four atoms. |
| CELL | COLVAR | Calculate the components of the simulation cell |
| CENTER | 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 multidimensionalscaling algorithm. |
| CLUSTER_DIAMETER | CONCOMP | Print out the diameter of one of the connected components |
| CLUSTER_DISTRIBUTION | CONCOMP | Calculate functions of the distribution of properties in your connected components. |
| CLUSTER_NATOMS | CONCOMP | Gives the number of atoms in the connected component |
| CLUSTER_PROPERTIES | CONCOMP | Calculate properties of the distribution of some quantities that are part of a connected component |
| CLUSTER_WITHSURFACE | MATRIXF | Take a connected component that was found using a clustering algorithm and create a new cluster that contains those atoms that are in the cluster together with those atoms that are within a certain cutoff of the cluster. |
| COLUMNSUMS | MATRIXF | Sum the columns of a contact matrix |
| 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 quantitieswith 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 ofcoordination 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 | An alias to the MATHEVAL function. |
| DEBUG | GENERIC | Set some debug options. |
| DENSITY | MCOLVAR | Calculate functions of the density of atoms as a function of the box. This allows one to calculatethe number of atoms in half the box. |
| DFSCLUSTERING | MATRIXF | Find the connected components of the matrix using the depth first search clustering algorithm. |
| DHENERGY | COLVAR | Calculate Debye-Huckel interaction energy among GROUPA and GROUPB. |
| DIHCOR | COLVAR | Measures the degree of similarity between dihedral angles. |
| 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 ofdistances 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) [60] methodon one or more collective variables. This method is alsocalled dynamic reference restraining(DRR) [98] . |
| 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 connnectivity 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). |
| 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 described in Ref [41] |
| 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. |
| ERMSD | COLVAR | Calculate eRMSD with respect to a reference structure. |
| EXTENDED_LAGRANGIAN | BIAS | Add extended Lagrangian. |
| EXTERNAL | BIAS | Calculate a restraint that is defined on a grid that is read during start up |
| FAKE | COLVAR | This is a fake colvar container used by cltools or various other actionsand just support input and period definition |
| FCCUBIC | MCOLVAR | Measure how similar the environment around atoms is to that found in a FCC structure. |
| FIND_CONTOUR | 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. |
| 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: |
| FUNCPATHMSD | FUNCTION | This function calculates path collective variables. |
| FUNCSUMHILLS | FUNCTION | This function is intended to be called by the command line tool sum_hillsand it is meant to integrate a HILLS file or an HILLS file interpreted asa histogram i a variety of ways. Therefore it is not expected that you use thisduring your dynamics (it will crash!) |
| GHOST | VATOM | Calculate the absolute position of a ghost atom with fixed coordinatesin the local reference frame formed by three atoms.The computed ghost atom is stored as a virtual atom that can be accessed inan atom list through the the label for the GHOST action that creates it. |
| GPROPERTYMAP | COLVAR | Property maps but with a more flexible framework for the distance metric being used. |
| GRADIENT | MCOLVARF | Calculate the gradient of the average value of a multicolvar value |
| 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 labelin definitions of CVs or virtual atoms. |
| GYRATION | COLVAR | Calculate the radius of gyration, or other properties related to it. |
| HBOND_MATRIX | MATRIX | Adjacency matrix in which two atoms are adjacent if there is a hydrogen bond between them. |
| HISTOGRAM | GRIDCALC | Accumulate the average probability density along a few CVs from a trajectory. |
| INCLUDE | GENERIC | Includes an external input file, similar to "#include" in C preprocessor. |
| INCYLINDER | VOLUMES | This quantity can be used to calculate functions of the distribution of collectivevariables for the atoms that lie in a particular, user-specified part of of the cell. |
| INENVELOPE | VOLUMES | This quantity can be used to calculate functions of the distribution of collectivevariables 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 collectivevariables 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 torsions 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. |
| 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 vectoron the atoms in the first coordination sphere. |
| LOCAL_Q4 | MCOLVARF | Calculate the local degree of order around an atoms by taking the average dot product between the q_4 vector on the central atom and the q_4 vectoron the atoms in the first coordination sphere. |
| LOCAL_Q6 | MCOLVARF | Calculate the local degree of order around an atoms by taking the average dot product between the q_6 vector on the central atom and the q_6 vectoron the atoms in the first coordination sphere. |
| LOWER_WALLS | BIAS | Defines a wall for the value of one or more collective variables, which limits the region of the phase space accessible during the simulation. |
| LWALLS | MCOLVARB | Add LOWER_WALLS restraints on all the multicolvar values |
| MATHEVAL | FUNCTION | Calculate a combination of variables using a matheval expression. |
| MAXENT | BIAS | Add a linear biasing potential on one or more variables f_{i}\left(\boldsymbol{x}\right) satisfying the maximum entropy principle as proposed in Ref. [2] . |
| MCOLV_COMBINE | MCOLVARF | Calculate linear combinations of multiple multicolvars |
| MCOLV_PRODUCT | MCOLVARF | Calculate a product of multiple multicolvars |
| 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 multicolvarso that one can compute the mean and so on for only those multicolvars within a certain range. |
| MFILTER_LESS | MFILTERS | This action can be used to filter the distribution of colvar values in a multicolvarso that one can compute the mean and so on for only those multicolvars less than a tolerance. |
| MFILTER_MORE | MFILTERS | This action can be used to filter the distribution of colvar values in a multicolvarso that one can compute the mean and so on for only those multicolvars more than a tolerance. |
| MOLECULES | MCOLVAR | Calculate the vectors connecting a pair of atoms in order to represent the orientation of a molecule. |
| MOLINFO | TOPOLOGY | This command is used to provide information on the molecules that are present in your system. |
| MOVINGRESTRAINT | BIAS | Add a time-dependent, harmonic restraint on one or more variables. |
| MTRANSFORM_BETWEEN | MTRANSFORMS | This action can be useed to transform the colvar values calculated by a multicolvar using a histogrambead |
| MTRANSFORM_LESS | MTRANSFORMS | This action can be useed to transform the colvar values calculated by a multicolvar using a switchingfunction |
| MTRANSFORM_MORE | MTRANSFORMS | This action can be useed to transform the colvar values calculated by a multicolvar using one minus a switchingfunction |
| MULTI-RMSD | DCOLVAR | Calculate the RMSD distance moved by a number of separated domains from their positions in a reference structure. |
| MULTICOLVARDENS | GRIDCALC | Evaluate the average value of a multicolvar on a grid. |
| MULTI_RMSD | DCOLVAR | An alias to the MULTI-RMSD function. |
| 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 atomsor ambiguous NOE. |
| OPT_AVERAGED_SGD | VES_OPTIMIZER | Averaged stochastic gradient decent with fixed step size. |
| OPT_DUMMY | VES_OPTIMIZER | Dummy optimizer for debugging. |
| OUTPUT_CLUSTER | CONCOMP | Output the indices of the atoms in one of the clusters identified by a clustering object |
| PARABETARMSD | COLVAR | Probe the parallel beta sheet content of your protein structure. |
| 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 ( see [82] and [80] ) for a number of provided eigenvectors and an average structure. Performs optimal alignment at every step and reports the rmsd so you know if you are far or close from the average structure.It takes the average structure and eigenvectors in form of a pdb.Note that beta and occupancy values in the pdb are neglected and all the weights are placed to 1 (differently from the RMSD colvar for example) |
| PCAVARS | COLVAR | Projection on principal component eigenvectors or other high dimensional linear subspace |
| PCS | ISDB_COLVAR | Calculates the Pseudocontact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization. |
| PIECEWISE | FUNCTION | Compute a piecewise straight line through its arguments that passes througha set of ordered control points. |
| PLANES | MCOLVAR | Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. |
| 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 Paramegnetic Resonance Enhancement intensity ratio between a spinlabel atom and a list of atoms . |
| PRINT | PRINTANALYSIS | Print quantities to a file. |
| PROPERTYMAP | COLVAR | Calculate generic property maps. |
| PUCKERING | COLVAR | Calculate sugar pseudorotation coordinates. |
| Q3 | MCOLVAR | Calculate 3rd order Steinhardt parameters. |
| Q4 | MCOLVAR | Calculate 4th order Steinhardt parameters. |
| Q6 | MCOLVAR | Calculate 6th order Steinhardt parameters. |
| RANDOM_EXCHANGES | GENERIC | Set random pattern for exchanges. |
| RDC | ISDB_COLVAR | Calculates the (Residual) Dipolar Coupling between two atoms. |
| READ | GENERIC | Read quantities from a colvar file. |
| RESCALE | ISDB_BIAS | Rescales 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. |
| REWEIGHT_BIAS | REWEIGHTING | Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored |
| REWEIGHT_METAD | REWEIGHTING | Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. |
| REWEIGHT_TEMP | REWEIGHTING | Calculate weights for ensemble averages allow for the computing of ensemble averages at temperatures lower/higher than that used in your original simulation. |
| RMSD | DCOLVAR | Calculate the RMSD with respect to a reference structure. |
| ROWSUMS | MATRIXF | Sum the rows of a adjacency matrix. |
| SAXS | ISDB_COLVAR | Calculates SAXS scattered intensity using the Debye equation. |
| 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 simplecubic structure. |
| SMAC | MCOLVARF | Calculate a variant on the SMAC collective variable discussed in [44] |
| 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.In particular it calculates and store as components the sum of the squared deviations, the correlation, theslope and the intercept of a linear fit. |
| TARGET | DCOLVAR | This function measures the pythagorean distance from a particular structure measured in the space defined by someset 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 Gaussians (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_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 productof 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 variablesfor 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 elsewere |
| 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. A new unit can be set by eitherspecifying how to convert from the plumed default unit into that new unit or by usingthe shortcuts described below. This directive MUST appear at the BEGINNING of theplumed.dat file. The same units must be used througout the plumed.dat file. |
| UPDATE_IF | PRINTANALYSIS | Conditional update of other actions. |
| UPPER_WALLS | BIAS | Defines a wall for the value of one or more collective variables, which limits the region of the phase space accessible during the simulation. |
| UWALLS | MCOLVARB | Add UPPER_WALLS restraints on all the multicolvar values |
| 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 FESs 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. |
| WHOLEMOLECULES | GENERIC | This action is used to rebuild molecules that can become split by the periodicboundary conditions. |
| WRAPAROUND | GENERIC | Rebuild periodic boundary conditions around chosen atoms. |
| 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 ofvalues such as the minimum, the number less than a certain quantity and so on. |
| XYDISTANCES | MCOLVAR | Calculate distance between a pair of atoms neglecting the z-component.You can then calculate functions of the distribution ofvalues such as the minimum, the number less than a certain quantity and so on. |
| 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.You can then calculate functions of the distribution ofvalues such as the minimum, the number less than a certain quantity and so on. |
| 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 ofvalues 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.You can then calculate functions of the distribution ofvalues such as the minimum, the number less than a certain quantity and so on. |
| 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 ofvalues 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. |
| 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 |
| gentemplate | TOOLS | gentemplate is a tool that you can use to construct template inputs for the variousactions |
| info | TOOLS | This tool allows you to obtain information about your plumed version |
| kt | TOOLS | Print out the value of k_BT 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 |
| pesmd | TOOLS | Pesmd allows one to do (biased) Langevin dynamics on a two-dimensional potential energy surface. |
| 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 |
1.8.14 
