BRIDGE_MATRIX

This is part of the adjmat module

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

contract shortcuts

w1: BRIDGE 
BRIDGING_ATOMS
The list of atoms that can form the bridge between the two interesting parts of the
structure.. 
=100-200 
GROUPA
. 
=1-10 
GROUPB
. 
=11-20 
SWITCH
The parameters of the two \ref switchingfunction in the above formula 
={RATIONAL R_0=0.2}  The BRIDGE action with label w1 calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=w1 
FILE
the name of the file on which to output these quantities 
=colvar The PRINT action with label 

w1_mat: BRIDGE_MATRIX 
SWITCH
The parameters of the two \ref switchingfunction in the above formula 
=RATIONAL,R_0=0.2 
BRIDGING_ATOMS
The list of atoms that can form the bridge between the two interesting parts of the
structure.. 
=100-200 
GROUPA
. 
=1-10 
GROUPB
. 
=11-20 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   
 Keyword   
 Description    

 w  
 COMPONENTS   
the weight of the connection   

 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   

 GROUPA  
. For more information on how to specify lists of atoms see Groups and Virtual Atoms   

 GROUPB  
. For more information on how to specify lists of atoms see Groups and Virtual Atoms   

Or alternatively by using



 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