Module: multicolvar

Description	Usage
tools for working with vectors of collective variables
Authors: Gareth Tribello

Details

THIS MODULE HAS BEEN INCLUDED FOR BACK COMPATIBILITY. ALL THE ACTIONS WITHIN IT ARE NOW SHORTCUTS. IF YOU USE THESE FUNCTIONALITIES WE WOULD STRONGLY ENCOURAGE YOU TO LOOK AT THE EXPANDED VERSIONS OF THESE INPUTS AND TO LEARN HOW THE NEWER AND MORE POWERFUL SYNTAX OPERATES. THE DOCUMENTATION THAT FOLLOWS IS COPIED FROM THE OLD MANUAL WHERE THIS NEW SYNTAX WAS NOT AVAILABLE

Oftentimes, when you do not need one of the collective variables described elsewhere in the manual, what you want instead is a function of a distribution of collective variables of a particular type. In other words, you would like to calculate a function something like this:

$s = \sum_i g[f(\{X\}_i)]$

In this expression $g$ is a function that takes in one argument and $f$ is a function that takes a set of atomic positions as argument. The symbol $\{X\}_i$ is used to indicate the fact that the function $f$ is evaluated for a number of different sets of atoms. If you would just like to output the values of all the various $f$ functions you can use the command DUMPMULTICOLVAR

This functionality is useful if you need to calculate a minimum distance or the number of coordination numbers greater than a 3.0. To avoid duplicating the code to calculate an angle or distance many times and to make it easier to implement very complex collective variables PLUMED provides these sort of collective variables using so-called MultiColvars. MultiColvars are named in this way because a single PLUMED action can be used to calculate a number of different collective variables. For instance the DISTANCES action can be used to calculate the minimum distance, the number of distances less than a certain value, the number of distances within a certain range... A more detailed introduction to multicolvars is provided in this 10-minute video.

To instruct PLUMED to calculate a multicolvar you give an instruction that looks something like this:

NAME <atoms involved> <parameters> <what am I calculating> TOL=0.001 LABEL=label

Oftentimes the simplest way to specify the atoms involved is to use multiple instances of the ATOMS keyword i.e. ATOMS1, ATOMS2, ATOMS3,... Separate instances of the quantity specified by NAME are then calculated for each of the sets of atoms. For example if the command issued contains the following:

Click on the labels of the actions for more information on what each action computes

dThe DISTANCES action with label d calculates the following quantities: Quantity    Type    Description  
d vector the DISTANCES between the each pair of atoms that were specified: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details ATOMS1the pairs of atoms that you would like to calculate the angles for=1,2 ATOMS2the pairs of atoms that you would like to calculate the angles for=3,4 ATOMS3the pairs of atoms that you would like to calculate the angles for=5,6
# PLUMED interprets the command:
# d: DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6
# as follows (Click the red comment above to revert to the short version of the input):
d_vatom1The CENTER_FAST action with label d_vatom1 calculates the following quantities: Quantity    Type    Description  
d_vatom1 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1,2
d_vatom2The CENTER_FAST action with label d_vatom2 calculates the following quantities: Quantity    Type    Description  
d_vatom2 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3,4
d_vatom3The CENTER_FAST action with label d_vatom3 calculates the following quantities: Quantity    Type    Description  
d_vatom3 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=5,6
d_grpThe GROUP action with label d_grp calculates the following quantities: Quantity    Type    Description  
d_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=d_vatom1,d_vatom2,d_vatom3
dThe DISTANCE action with label d calculates the following quantities: Quantity    Type    Description  
d vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=3,4 ATOMS3the pair of atom that we are calculating the distance between=5,6
# --- End of included input ---

The distances between atoms 1 and 2, atoms 3 and 4, and atoms 5 and 6 are calculated. Obviously, generating this sort of input is rather tedious so short cuts are also available many of the collective variables. These are described on the manual pages for the actions.

After specifying the atoms involved you sometimes need to specify some parameters that required in the calculation. For instance, for COORDINATIONNUMBER - the number of atoms in the first coordination sphere of each of the atoms in the system - you need to specify the parameters for a switching function (see LESS_THAN) that will tell us whether or not an atom is in the first coordination sphere. Details as to how to do this are provided on the manual pages.

Once you have specified the base quantities that are to be calculated from the atoms involved and any parameters you need to specify what function of these base quantities is to be calculated. For most multicolvars you can calculate the minimum, the number less than a target value, the number within a certain range, the number more than a target value and the average value directly.

Multicolvar functions and biases

In older versions of PLUMED there were actions that took the label of a multicolvar as input and computed things from the vector of CVs directly from them. In newer versions this functionality is easier to use as the multicolvars are shortcuts. You thus use the outputs from the commmands that output the vectors of CV values in the input to other actions directly.

Actions

The following actions are part of this module

Name	Description	Tags
ALPHABETA	Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values.	MCOLVAR
ANGLES	Calculate functions of the distribution of angles.	COLVAR
COORD_ANGLES	Calculate functions of the distribution of angles between bonds in the first coordination spheres of a set of atoms	MCOLVAR
DIHCOR	Measures the degree of similarity between dihedral angles.	COLVAR
DISTANCES	Calculate the distances between multiple piars of atoms	MCOLVAR
DUMPMULTICOLVAR	Dump atom positions and a vector of values to a file.	MCOLVAR
INPLANEDISTANCES	Calculate distances in the plane perpendicular to an axis	MCOLVAR
MFILTER_LESS	Apply a switching function to the input vector.	MCOLVAR
MFILTER_MORE	Apply one minus a switching function to the input vector.	MCOLVAR
PLANES	Calculate the components of the normals to the planes containing groups of three atoms.	MCOLVAR
TORSIONS	Calculate whether or not a set of torsional angles are within a particular range.	MCOLVAR
UWALLS	Add lower walls to a vector of quantities	MCOLVAR
XANGLES	Calculate the angle between an arbitrary vector and the positive x direction	COLVAR
XDISTANCES	Calculate the x components of the vectors connecting one or many pairs of atoms.	MCOLVAR
XYTORSIONS	Calculate the torsional angle around the x axis between an arbitrary vector and the positive y direction	COLVAR
XZTORSIONS	Calculate the torsional angle around the x axis between an arbitrary vector and the positive z direction	COLVAR
YANGLES	Calculate the angle between an arbitrary vector and the positive y direction	COLVAR
YDISTANCES	Calculate the y components of the vectors connecting one or many pairs of atoms.	MCOLVAR
YXTORSIONS	Calculate the torsional angle around the y axis between an arbitrary vector and the positive x direction	COLVAR
YZTORSIONS	Calculate the torsional angle around the y axis between an arbitrary vector and the positive z direction	COLVAR
ZANGLES	Calculate the angle between an arbitrary vector and the positive z direction	COLVAR
ZDISTANCES	Calculate the z components of the vectors connecting one or many pairs of atoms.	MCOLVAR
ZXTORSIONS	Calculate the torsional angle around the z axis between an arbitrary vector and the positive x direction	COLVAR
ZYTORSIONS	Calculate the torsional angle around the z axis between an arbitrary vector and the positive y direction	COLVAR

Quantity	Type	Description
d	vector	the DISTANCES between the each pair of atoms that were specified

Quantity	Type	Description
d	vector	the DISTANCE for each set of specified atoms