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.

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. |

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. |