Index of Actions

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:

• Collective variables tells you about the ways that you can calculate functions of the positions of the atoms.
• Analysis tells you about the various forms of analysis you can run on trajectories using PLUMED.
• Bias tells you about the methods that you can use to bias molecular dynamics simulations with PLUMED.

# Full list of actions

 ABMD BIAS Adds a ratchet-and-pawl like restraint on one or more variables. 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. ANGLES MCOLVAR Calculate functions of the distribution of angles . ANGLE COLVAR Calculate an angle. ANTIBETARMSD COLVAR Probe the antiparallel beta sheet content of your protein structure. AROUND MCOLVARF 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. BIASVALUE BIAS Takes the value of one variable and use it as a bias BRIDGE MCOLVAR Calculate the number of atoms that bridge two parts of a structure CAVITY MCOLVARF This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a box defined by the positions of four atoms. CELL COLVAR Calculate the components of the simulation cell CENTER VATOM Calculate the center for a group of atoms, with arbitrary weights. CH3SHIFTS COLVAR This collective variable calculates a scoring function based on the comparison of calculated andexperimental methyl chemical shifts. CLASSICAL_MDS ANALYSIS Create a low-dimensional projection of a trajectory using the classical multidimensional scaling algorithm. COMBINE FUNCTION Calculate a polynomial combination of a set of other variables. COMMITTOR ANALYSIS Does a committor analysis. COM VATOM Calculate the center of mass for a group of atoms. CONSTANT COLVAR Return a constant quantity. CONTACTMAP COLVAR Calculate the distances between a number of pairs of atoms and transform each distance by a switching function.The transformed distance can be compared with a reference value in order to calculate the squared distancebetween two contact maps. Each distance can also be weighted for a given value. CONTACTMAP can be used togetherwith FUNCPATHMSD to define a path in the contactmap space. 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. COORDINATION COLVAR Calculate coordination numbers. CS2BACKBONE COLVAR This collective variable calculates a scoring function based on the comparison of backcalculated andexperimental backbone chemical shifts for a protein (CA, CB, C', H, HA, N). 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. DFSCLUSTERDIAMETER MCOLVARF Retrieve the size of a cluster. This quantity is NOT differentiable. DFSCLUSTERING MCOLVARF Cluster atoms based on their proximities and find the average properties of those atomsin a cluster. DFSMAXCLUSTER MCOLVARF Find the connected components and determine the maximum size of the clusters in your system using a smooth function DFSNUMEROFCLUSTERS MCOLVARF Find the number of clusters that have a size larger than a certain cutoff DHENERGY COLVAR Calculate Debye-Huckel interaction energy among GROUPA and GROUPB. DIHCOR COLVAR Measures the degree of similarity between dihedral angles. DIPOLE COLVAR Calculate the dipole moment for a group 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 COLVAR Calculate the distance between a pair of atoms. driver TOOLS driver is a tool that allows one to to use plumed to post-process an existing trajectory. DRMSD DCOLVAR Calculate the distance RMSD with respect to a reference structure. DUMPATOMS ANALYSIS Dump selected atoms on a file. DUMPDERIVATIVES ANALYSIS Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). DUMPFORCES ANALYSIS Dump the force acting on one of a values in a file. DUMPMASSCHARGE ANALYSIS Dump masses and charges on a selected file. DUMPMULTICOLVAR ANALYSIS Dump atom positions and multicolvar on a file. DUMPPROJECTIONS ANALYSIS Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). EFFECTIVE_ENERGY_DRIFT GENERIC Print the effective energy drift described in Ref [21] ENERGY COLVAR Calculate the total energy of the simulation box. ENSEMBLE FUNCTION Calculates the replica averaging of a collective variable over multiple replicas. 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 FIT_TO_TEMPLATE GENERIC This action is used to align a molecule to a template. 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. 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 as a histogram i a variety of ways. Therefore it is not expected that you use this during your dynamics (it will crash!) gentemplate TOOLS gentemplate is a tool that you can use to construct template inputs for the variousactions 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. 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. HISTOGRAM ANALYSIS Calculate the probability density as a function of a few CVs either using kernel density estimation, or a discretehistogram estimation. IMD GENERIC Use interactive molecular dynamics with VMD INCLUDE GENERIC Includes an external input file, similar to "#include" in C preprocessor. INCYLINDER MCOLVARF 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. info TOOLS This tool allows you to obtain information about your plumed version INPLANEDISTANCES MCOLVAR Calculate distances in the plane perpendicular to an axis kt TOOLS Print out the value of $$k_BT$$ at a particular temperature LOAD GENERIC Loads a library, possibly defining new actions. 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. manual TOOLS manual is a tool that you can use to construct the manual page for a particular action MATHEVAL FUNCTION Calculate a combination of variables using a matheval expression. METAD BIAS Used to performed MetaDynamics on one or more collective variables. MFILTER_BETWEEN MCOLVARF This action can be used to filter the distribution of colvar values in a multicolvar so that one can compute the mean and so on for only those multicolvars within a certain range. MFILTER_LESS MCOLVARF This action can be used to filter the distribution of colvar values in a multicolvar so that one can compute the mean and so on for only those multicolvars less than a tolerance. MFILTER_MORE MCOLVARF This action can be used to filter the distribution of colvar values in a multicolvar so that one can compute the mean and so on for only those multicolvars more than a tolerance. MOLECULES MCOLVAR Calculate the vectors connecting a pair of atoms in order to represent the orientation of a molecule. MOLINFO TOPOLOGY This command is used to provide information on the molecules that are present in your system. MOVINGRESTRAINT BIAS Add a time-dependent, harmonic restraint on one or more variables. MULTICOLVARDENS ANALYSIS Dump atom positions and multicolvar on a file. MULTI-RMSD DCOLVAR Calculate the RMSD distance moved by a number of separated domains from their positions in a reference structure. NLINKS MCOLVARF Calculate number of pairs of atoms/molecules that are "linked" NOE COLVAR Calculates the deviation of current distances from experimental NOE derived distances. PARABETARMSD COLVAR Probe the parallel beta sheet content of your protein structure. PATHMSD COLVAR This Colvar calculates path collective variables. PATH COLVAR Path collective variables with a more flexible framework for the distance metric being used. PBMETAD BIAS Used to performed Parallel Bias MetaDynamics. PCARMSD DCOLVAR Calculate the PCA components ( see [46] and [44] ) 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 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. POSITION COLVAR Calculate the components of the position of an atom. PRINT ANALYSIS Print quantities to a file. PROPERTYMAP COLVAR Calculate generic property maps. PUCKERING COLVAR Calculate the Nucleic Acid 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 COLVAR Calculates the Residual Dipolar Coupling between two atoms. READ GENERIC Read quantities from a colvar file. RESTART GENERIC Activate restart. RESTRAINT BIAS Adds harmonic and/or linear restraints on one or more variables. RMSD DCOLVAR Calculate the RMSD with respect to a reference structure. SIMPLECUBIC MCOLVAR Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simplecubic structure. simplemd TOOLS simplemd allows one to do molecular dynamics on systems of Lennard-Jones atoms. SORT FUNCTION This function can be used to sort colvars according to their magnitudes. SPRINT MCOLVARF Calculate SPRINT topological variables. sum_hills TOOLS sum_hills is a tool that allows one to to use plumed to post-process an existing hills/colvar file TARGET DCOLVAR This function measures the pythagorean distance from a particular structure measured in the space defined by some set of collective variables. TEMPLATE COLVAR This file provides a template for if you want to introduce a new CV. TETRAHEDRALPORE MCOLVARF TETRAHEDRAL MCOLVAR Calculate the degree to which the environment about ions has a tetrahedral order. TIME GENERIC retrieve the time of the simulation to be used elsewere TORSIONS MCOLVAR Calculate whether or not a set of torsional angles are within a particular range. TORSION COLVAR Calculate a torsional angle. 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 the plumed.dat file. The same units must be used througout the plumed.dat file. 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 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. 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. 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. 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. 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. 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.