Glossary 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:

# 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 CELL COLVAR Calculate the components of the simulation cell CENTER VATOM Calculate the center for a group of atoms, with arbitrary weights. COMBINE FUNCTION Calculate a polynomial combination of a set of other variables. 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 set of reference values in order to calculate the squared distancebetween two contact maps. 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. DHENERGY COLVAR Calculate Debye-Huckel interaction energy among GROUPA and GROUPB. DIPOLE COLVAR Calcualte 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.By default the distance is computed taking into account periodicboundary conditions. This behavior can be changed with the NOPBC flag.Moreover, single components (x,y, and z) can be also computed. driver TOOLS driver is a tool that allows one to to use plumed to post-process an existing trajectory. DRMSD COLVAR 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. DUMPPROJECTIONS ANALYSIS Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). ENERGY COLVAR Calculate the total energy of the simulation box. 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 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. 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 using kernel density estimation IMD GENERIC Use interactive molecular dynamics with VMD INCLUDE GENERIC Includes an external input file, similar to "#include" in C preprocessor. info TOOLS This tool allows you to obtain information about your plumed version LOAD GENERIC Loads a library, possibly defining new actions. LOWER_WALLS BIAS The LOWER_WALLS and UPPER_WALLS keywords define 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. 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. PARABETARMSD COLVAR Probe the parallel beta sheet content of your protein structure. PATHMSD COLVAR This Colvar calculates path collective variables. PIECEWISE FUNCTION Compute a piecewise straight line through its arguments that passes througha set of ordered control points. PRINT ANALYSIS Print quantities to a file. PROPERTYMAP COLVAR Calculate generic property maps. RANDOM_EXCHANGES GENERIC Set random pattern for exchanges. 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 COLVAR Calculate the RMSD with respect to a reference 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. sum_hills TOOLS sum_hills is a tool that allows one to to use plumed to post-process an existing hills/colvar file TARGET FUNCTION 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. TIME GENERIC retrieve the time of the simulation to be used elsewere 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 The LOWER_WALLS and UPPER_WALLS keywords define a wall for the value of one or more collective variables, which limits the region of the phase space accessible during the simulation. 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.

# Dictionary

 BiasRepresentation INTERNAL An internal tool in plumed that is used to represent a bias histogrambead INTERNAL A function that can be used to calculate whether quantities are between fixed upper and lower bounds. kernelfunctions INTERNAL Functions that are used to construct histograms reweighting INTERNAL Calculate free energies from a biassed/higher temperature trajectory. switchingfunction INTERNAL Functions that measure whether values are less than a certain quantity.