Module: colvar
| Description | Usage |
|---|---|
| various core collective variables that can be used to analyse or bias simulations | |
| Authors: The PLUMED core developers |   |
Details
Chemical systems contain an enormous number atoms, which, in most cases makes it simply impossible for us to understand anything by monitoring the atom positions directly. Consequently, we introduce Collective variables (CVs) that describe the chemical processes we are interested in and monitor these simpler quantities instead. These CVs are used in many of the methods implemented in PLUMED - there values can be monitored using PRINT, Functions of them can be calculated using the methods in the function module, they can be analyzed using the tools in the dimred, gridtools or generic moeuls or they can be biased using the tools in the bias module. Before doing any of these things, however, we first have to tell PLUMED how to calculate them.
The simplest collective variables that are implemented in PLUMED take in a set of atomic positions and output one or multiple scalar CV values. Many of the variables that operate like this are provided in this module.
Please be aware that many other modules contain implementations other collective variables. In other words, the colvar module does not contain implementations of all the collectivar variables that are available in PLUMED.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| ANGLE | Calculate one or multiple angle/s. | COLVAR |
| CELL | Get the components of the simulation cell | COLVAR |
| CHARGE | Get the charges of one or multiple atoms | MCOLVAR |
| CONTACTMAP | Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. | COLVAR |
| COORDINATION | Calculate coordination numbers. | COLVAR |
| DHENERGY | Calculate Debye-Huckel interaction energy between the atoms in GROUPA and GROUPB. | COLVAR |
| DIHEDRAL_CORRELATION | Measure the correlation between a pair of dihedral angles | COLVAR |
| DIMER | This CV computes the dimer interaction energy for a collection of dimers. | COLVAR |
| DIPOLE | Calculate the dipole moment for a group of atoms. | COLVAR |
| DISTANCE | Calculate the distance/s between pairs of atoms. | COLVAR |
| DRMSD | Calculate the distance RMSD with respect to a reference structure. | DCOLVAR |
| EEFSOLV | Calculates EEF1 solvation free energy for a group of atoms. | COLVAR |
| ENERGY | Calculate the total potential energy of the simulation box. | COLVAR |
| ERMSD | Calculate eRMSD with respect to a reference structure. | COLVAR |
| EXTRACV | Allow PLUMED to use collective variables computed in the MD engine. | COLVAR |
| FAKE | This is a fake colvar container that is used by cltools or various other actions that supports input and period definitions | COLVAR |
| GHBFIX | Calculate the GHBFIX interaction energy between GROUPA and GROUPB | COLVAR |
| GYRATION | Calculate the radius of gyration, or other properties related to it. | COLVAR |
| GYRATION_TENSOR | Calculate the gyration tensor using a user specified vector of weights | MCOLVAR |
| MASS | Get the mass of one or multiple atoms | MCOLVAR |
| MULTI_RMSD | Calculate RMSD distances for different domains and combine them. | DCOLVAR |
| PATHMSD | This Colvar calculates path collective variables. | COLVAR |
| PCARMSD | Calculate the PCA components for a number of provided eigenvectors and an average structure. | DCOLVAR |
| PLANE | Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. | COLVAR |
| POSITION | Calculate the components of the position of an atom or atoms. | COLVAR |
| PROJECTION_ON_AXIS | Calculate a position based on the projection along and extension from a defined axis. | COLVAR |
| PROPERTYMAP | Calculate generic property maps. | COLVAR |
| PUCKERING | Calculate sugar pseudorotation coordinates. | COLVAR |
| RMSD | Calculate the RMSD with respect to a reference structure. | DCOLVAR |
| TEMPLATE | This file provides a template for if you want to introduce a new CV. | COLVAR |
| TORSION | Calculate one or multiple torsional angles. | COLVAR |
| VOLUME | Calculate the volume the simulation box. | COLVAR |