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:

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. |

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. |

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. |

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