Modules that make up PLUMED Version 2.11
The functionality in PLUMED is split up between a collection of modules. Each of these modules contains a collection of actions, shortcuts and command line tools. Some of these modules must be present every time PLUMED is compiled, others are not essential but are still compiled by default unless you explicitly tell PLUMED not to compile by using:
./configure --disable-module=module-name
The remainder of the modules are not compiled unless you explicitly request PLUMED to include that module in your compilation by using the command:
./configure --enable-module=module-name
The table below lists all the available modules and tells you whether they are always compiled, on by default or off by default. An alternative, graphical view of this information is available here.
| Name | Description | Authors | Type |
|---|---|---|---|
| bias | bias potentials that can be used to force rare events to occur in MD simulations | The PLUMED core developers | default-on |
| generic | generic features of PLUMED many of which are for printing data to files | The PLUMED core developers | default-on |
| mapping | actions for definining linear and curvilinear paths and manifolds in a higher dimensional space | Gareth Tribello | default-off |
| multicolvar | tools for working with vectors of collective variables | Gareth Tribello | default-on |
| secondarystructure | variables for detecting the degree of secondary structure in a protein | Gareth Tribello | default-on |
| colvar | various core collective variables that can be used to analyse or bias simulations | The PLUMED core developers | default-on |
| annfunc | an implementation of a fully-connected feedforward neural network | Wei Chan and Andrew Ferguson | default-off |
| vatom | actions for calculating the positions of virtual atoms | The PLUMED core developers | default-on |
| volumes | tools for calculating whether atoms are within a certain part of the simulation cell or not | Gareth Tribello | default-off |
| dimred | tools for performing dimensionality reduction | Gareth Tribello | default-off |
| symfunc | tools for calculating symmetry functions that measure the degree of order in the coordination sphere around atoms | Gareth Tribello | default-off |
| function | actions that take arguments as input and that return values | The PLUMED core developers | default-on |
| ves | implementations of methods based on Variationally Enhanced Sampling (VES) | Omar Valsson, Michele Invernizzi, Pablo Piaggi and Benjamin Pampel | default-off |
| crystdistrib | order parameters for studying the formation of molecular crystals | Jake McKibbin, Gareth Tribello and Erik Santiso | default-off |
| adjmat | methods for calculating adjacency matrices | Gareth Tribello | default-off |
| isdb | tools for doing integrative structural and dynamical biology | Max Bonomi and Carlo Camilloni | default-on |
| clusters | tools for using depth first search clustering to find the largest connected component in an adjacency matrix | Gareth Tribello, Federico Giberti, Matteo Salvalaglio and Gabriele Sosso | default-off |
| landmarks | various tools for selecting a subset of points from an input vector/matrix | Gareth Tribello | default-off |
| valtools | tools for manipulating the values that are passed between actions | Gareth Tribello | always |
| gridtools | tools for manipulating functions that are stored on grids | Gareth Tribello | default-on |
| matrixtools | tools for constructing and manipulating matrices | Gareth Tribello | default-on |
| refdist | tools for calculating the distance between trajectory frames | Gareth Tribello | default-on |
| contour | actions that take functions as grid as input and that find isocontours in these functions | Gareth Tribello | default-off |
| core | PLUMED's core functionalities for interfacing with MD codes and building actions | The PLUMED core developers | always |
| drr | an implementation of the extended-system adaptive biasing force (eABF) method | Haochuan Chen and Haohao Fu | default-off |
| opes | On-the-fly Probability Enhanced Sampling (OPES) | Michele Invernizzi | default-off |
| eds | Methods for incorporating additional information about CVs into MD simulations by adaptively determined linear bias parameters | Glen Hocky and Andrew White | default-off |
| envsim | the environmental similarity symmetry function that can be used for probing crystallinity in atomistic systems | Pablo Piaggi and Gareth Tribello | default-off |
| fisst | An implementation of infinite switch simulated tempering in force (FISST) | Glen Hocky | default-off |
| fourier | tools for performing a 2D fast fourier transform of a function on a grid | Edoardo Baldi and Gareth Tribello | default-off |
| funnel | a collective variable and a bias action necessary to perform Funnel-Metadynamics on Molecular Dynamics simulations | Stefano Raniolo and Vittorio Limongelli | default-off |
| membranefusion | a set of collective variables that induces different steps in the MF process | Ary Lautaro Di Bartolo and Diego Masone | default-off |
| pamm | implementations of the pamm methodology one application of which can be to determine if atoms are hydrogen bonded or not | Gareth Tribello | default-off |
| setup | actions that are used in setup to set units, specify that we are restarting a simulation or to load additional functionality | The PLUMED core developers | default-on |
| logmfd | Method for enhanced sampling and for free energy calculations along collective variables | Tetsuya Morishita, Naoki Watanabe | default-off |
| maze | enhanced sampling methods for studying ligand unbinding from protein tunnels | Jakub Rydzewski | default-off |
| metatomic | Using arbitrary machine learning models as collective variables | Guillaume Fraux | default-off |
| piv | an implementation of the permutation invariant collective variable | S. Pipolo and F. Pietrucci | default-off |
| pytorch | an interface between PLUMED and the PyTorch machine learning library | Luigi Bonati | default-off |
| s2cm | S2 contact model collective variable (S2CM) | Omar Valsson | default-off |
| sasa | Solvent Accessible Surface Area collective variable (SASA) | Andrea Arsiccio | default-off |
| sizeshape | Linear projection in size and shape space | Subarna Sasmal and Glen M Hocky | default-off |
| sprint | an implementation of the SPRINT CV | Gareth Tribello | default-off |
| wham | an implementation of the binless wham technique | Gareth Tribello | default-off |
| cltools | PLUMED's suite of command line tools | The PLUMED core developers | default-on |