It is only available if you configure PLUMED with ./configure –enable-modules=adjmat . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.
Calculate the number of atoms that bridge two parts of a structure
This quantity calculates:
\[ f(x) = \sum_{ijk} s_A(r_{ij})s_B(r_{ik})
\]
where the sum over \(i\) is over all the ``bridging atoms" and \(s_A\) and \(s_B\) are switchingfunction.
Examples
The following example instructs plumed to calculate the number of water molecules that are bridging between atoms 1-10 and atoms 11-20 and to print the value to a file
Click on the labels of the actions for more information on what each action computes
w1: BRIDGEBRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the
structure.. =100-200 GROUPA. =1-10 GROUPB. =11-20 SWITCHThe parameters of the two switchingfunction in the above formula ={RATIONAL R_0=0.2} The BRIDGE action with label w1 calculates a single scalar valuePRINTARGthe input for this action is the scalar output from one or more other actions. =w1FILEthe name of the file on which to output these quantities =colvar The PRINT action with label
w1_mat: BRIDGE_MATRIXSWITCHThe parameters of the two switchingfunction in the above formula =RATIONAL,R_0=0.2 The BRIDGE_MATRIX action with label w1_mat
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
a matrix containing the weights for the bonds between each pair of atoms
In addition the following quantities can be calculated by employing the keywords listed below
Quantity
Keyword
Description
w
COMPONENTS
a matrix containing the weights for the bonds between each pair of atoms
x
COMPONENTS
the projection of the bond on the x axis
y
COMPONENTS
the projection of the bond on the y axis
z
COMPONENTS
the projection of the bond on the z axis
The atoms involved can be specified using
GROUP
the atoms for which you would like to calculate the adjacency matrix. For more information on how to specify lists of atoms see Groups and Virtual Atoms
the atoms for which you would like to calculate the adjacency matrix. This is a depracated syntax that is equivalent to GROUP. You are strongly recommened to use GROUP instead of ATOMS.
Or alternatively by using
BRIDGING_ATOMS
The list of atoms that can form the bridge between the two interesting parts of the structure.. For more information on how to specify lists of atoms see Groups and Virtual Atoms
Compulsory keywords
NL_CUTOFF
( default=0.0 ) The cutoff for the neighbor list. A value of 0 means we are not using a neighbor list
NL_STRIDE
( default=1 ) The frequency with which we are updating the atoms in the neighbor list
Options
SERIAL
( default=off ) do the calculation in serial. Do not parallelize
COMPONENTS
( default=off ) also calculate the components of the vector connecting the atoms in the contact matrix
NOPBC
( default=off ) don't use pbc
SWITCH
The parameters of the two switchingfunction in the above formula
SWITCHA
The switchingfunction on the distance between bridging atoms and the atoms in group A
SWITCHB
The switchingfunction on the distance between the bridging atoms and the atoms in group B
1.13.2