Shortcut: BRIDGE

Module	adjmat
Description	Usage
Calculate the number of briding atoms between two groups
output value	type
the number of bridging atoms between the two groups	scalar

Details and examples

Calculate the number of briding atoms between two groups

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 switching functions.

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

w1The BRIDGE action with label w1 calculates the following quantities: Quantity    Type    Description  
w1 scalar the number of bridging atoms between the two groups: BRIDGECalculate the number of briding atoms between two groups This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1-10 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=11-20 SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
# PLUMED interprets the command:
# w1: BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 SWITCH={RATIONAL R_0=0.2}
# as follows (Click the red comment above to revert to the short version of the input):
w1_matThe BRIDGE_MATRIX action with label w1_mat calculates the following quantities: Quantity    Type    Description  
w1_mat matrix a matrix containing the weights for the bonds between each pair of atoms: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure More details SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}  BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1-10 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=11-20
w1The SUM action with label w1 calculates the following quantities: Quantity    Type    Description  
w1 scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=w1_mat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=w1 FILEthe name of the file on which to output these quantities=colvar

You can use the following input instead to calculate the number of atoms that bridge between the 45 pairs of distinct pairs of atoms that can be selected from the set of atoms with indexes between 1 and 10.

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

w1The BRIDGE action with label w1 calculates the following quantities: Quantity    Type    Description  
w1 scalar the number of bridging atoms between the two groups: BRIDGECalculate the number of briding atoms between two groups This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10 SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
# PLUMED interprets the command:
# w1: BRIDGE BRIDGING_ATOMS=100-200 GROUP=1-10 SWITCH={RATIONAL R_0=0.2}
# as follows (Click the red comment above to revert to the short version of the input):
w1_matThe BRIDGE_MATRIX action with label w1_mat calculates the following quantities: Quantity    Type    Description  
w1_mat matrix a matrix containing the weights for the bonds between each pair of atoms: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure More details SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}  BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPthe atoms for which you would like to calculate the adjacency matrix=1-10
w1The SUM action with label w1 calculates the following quantities: Quantity    Type    Description  
w1 scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=w1_mat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=w1 FILEthe name of the file on which to output these quantities=colvar

In the above inputs the switching functions $s_A$ and $s_B$ are identical. If you want to use two different switching functions you would use an input like the one shown below:

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

w1The BRIDGE action with label w1 calculates the following quantities: Quantity    Type    Description  
w1 scalar the number of bridging atoms between the two groups: BRIDGECalculate the number of briding atoms between two groups This action is a shortcut. More details ...
  BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1-10 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=11-20
  SWITCHAThe switching function on the distance between bridging atoms and the atoms in group A. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
  SWITCHBThe switching function on the distance between the bridging atoms and the atoms in group B. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.4}
...
# PLUMED interprets the command:
# w1: BRIDGE ...
#   BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20
#   SWITCHA={RATIONAL R_0=0.2}
#   SWITCHB={RATIONAL R_0=0.4}
# ...
# as follows (Click the red comment above to revert to the short version of the input):
w1_matThe BRIDGE_MATRIX action with label w1_mat calculates the following quantities: Quantity    Type    Description  
w1_mat matrix a matrix containing the weights for the bonds between each pair of atoms: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure More details SWITCHAThe switching function on the distance between bridging atoms and the atoms in group A. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2} SWITCHBThe switching function on the distance between the bridging atoms and the atoms in group B. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.4}  BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=100-200 GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1-10 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=11-20
w1The SUM action with label w1 calculates the following quantities: Quantity    Type    Description  
w1 scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=w1_mat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=w1 FILEthe name of the file on which to output these quantities=colvar

With this input an atom is calculated as bridging if it is (approximately) within 0.2 nm of one of the atoms in GROUPA and within 0.4 nm of one of the atoms in GROUPB.

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
GROUP	atoms	the atoms for which you would like to calculate the adjacency matrix
GROUPA	atoms	when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB	atoms	when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
BRIDGING_ATOMS	atoms	The list of atoms that can form the bridge between the two interesting parts of the structure

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
GROUP	input	none	the atoms for which you would like to calculate the adjacency matrix
GROUPA	input	none	when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB
GROUPB	input	none	when you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA
BRIDGING_ATOMS	input	none	The list of atoms that can form the bridge between the two interesting parts of the structure
SWITCH	optional	not used	The parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.
SWITCHA	optional	not used	The switching function on the distance between bridging atoms and the atoms in group A. Options for this keyword are explained in the documentation for LESS_THAN.
SWITCHB	optional	not used	The switching function on the distance between the bridging atoms and the atoms in group B. Options for this keyword are explained in the documentation for LESS_THAN.

Quantity	Type	Description
w1	scalar	the number of bridging atoms between the two groups