It is only available if you configure PLUMED with ./configure –enable-modules=volumes . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

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.

Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three dimensional space. For example, if we have the coordination numbers for all the atoms in the system each coordination number can be assumed to lie on the position of the central atom. Because each base quantity can be assigned to a particular point in space we can calculate functions of the distribution of base quantities in a particular part of the box by using:

where the sum is over the collective variables, \(s_i\), each of which can be thought to be at \( (x_i,y_i,z_i)\). The function \( w(x_i,y_i,z_i) \) measures whether or not the system is in the subregion of interest. It is equal to:

where \(K\) is one of the kernel functions described on histogrambead and \(\sigma\) is a bandwidth parameter. The function \((s_i)\) can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.

When AROUND is used with the DENSITY action the number of atoms in the specified region is calculated

Examples

The following commands tell plumed to calculate the average coordination number for the atoms that have x (in fractional coordinates) within 2.0 nm of the com of mass c1. The final value will be labeled s.mean.

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

the numerical indexes for the set of atoms in the group.

=1-100 The GROUP action with label c_grp defines a group of atoms so that they can be referred to later in the inputc_mat: CONTACT_MATRIX

GROUP

specifies the list of atoms that should be assumed indistinguishable.

=1-100

R_0

could not find this keyword

=1.0

D_0

could not find this keyword

=0.0

NN

compulsory keyword ( default=6 )
The n parameter of the switching function

=6

MM

compulsory keyword ( default=0 )
The m parameter of the switching function; 0 implies 2*NN

=0 The CONTACT_MATRIX action with label c_mat calculates a single scalar valuec_ones: ONES

SIZE

compulsory keyword
the number of ones that you would like to create

=100 The ONES action with label c_ones calculates a single scalar valuec: MATRIX_VECTOR_PRODUCT

ARG

compulsory keyword
the label for the matrix and the vector/scalar that are being multiplied.

=c_mat,c_onesThe MATRIX_VECTOR_PRODUCT action with label c calculates a single scalar valuec_caverage: MEAN

ARG

compulsory keyword
the values input to this function

=c

PERIODIC

compulsory keyword
if the output of your function is periodic then you should specify the periodicity
of the function.

=NO The MEAN action with label c_caverage calculates a single scalar values_grp: GROUP

ATOMS

the numerical indexes for the set of atoms in the group.

=cThe GROUP action with label s_grp defines a group of atoms so that they can be referred to later in the inputs_prod: CUSTOM

ARG

compulsory keyword
the values input to this function

=c,s

FUNC

compulsory keyword
the function you wish to evaluate

=x*y

PERIODIC

compulsory keyword
if the output of your function is periodic then you should specify the periodicity
of the function.

=NO The CUSTOM action with label s_prod

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity

Description

.#!value

sum of values of input CVs in regin of interest

In addition the following quantities can be calculated by employing the keywords listed below

Quantity

Keyword

Description

lessthan

LESS_THAN

the number of cvs in the region of interest that are less than a certain threshold

morethan

MORE_THAN

the number of cvs in the region of interest that are more than a certain threshold

between

BETWEEN

the number of cvs in the region of interest that are within a certain range

sum

SUM

the sum of all the colvars weighted by the function that determines if we are in the region

mean

MEAN

the average values of the colvar in the region of interest

The atoms involved can be specified using

ATOMS

the group of atoms that you would like to investigate. For more information on how to specify lists of atoms see Groups and Virtual Atoms

ORIGIN

the atom whose vicinity we are interested in examining. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Or alternatively by using

ATOM

an alternative to ORIGIN

Compulsory keywords

SIGMA

the width of the function to be used for kernel density estimation

KERNEL

( default=gaussian ) the type of kernel function to be used

XLOWER

( default=0.0 ) the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).

XUPPER

( default=0.0 ) the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).

YLOWER

( default=0.0 ) the lower boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).

YUPPER

( default=0.0 ) the upper boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).

ZLOWER

( default=0.0 ) the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).

ZUPPER

( default=0.0 ) the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).

Options

SERIAL

( default=off ) do the calculation in serial. Do not parallelize

OUTSIDE

( default=off ) calculate quantities for colvars that are on atoms outside the region of interest

SUM

( default=off ) calculate the sum of all the quantities.

MEAN

( default=off ) calculate the average value of the colvar inside the region of interest

DATA

the label of an action that calculates multicolvars. Weighted sums based on the location of the colvars calculated by this action will be calcualted

LESS_THAN

calcualte the number of colvars that are inside the region of interest and that are less than a certain threshold

MORE_THAN

calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold

BETWEEN

calculate the number of colvars that are inside the region of interest and that have a CV value that is between a particular set of bounds