Action: BRIDGE_MATRIX

Module	adjmat
Description	Usage
Calculate the number of atoms that bridge two parts of a structure
output value	type
a matrix containing the weights for the bonds between each pair of atoms	matrix

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Input

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

Further details and examples

Calculate the number of atoms that bridge two parts of a structure

This adjacency matrix is used to implement the BRIDGE shortcut. The action outputs a adjacency matrix in the same way as CONTACT_MATRIX. However, the $j,k$ element of the adjacency matrix is calculated using:

\f[ f(x) = \sum_{ijk} s_A(r_{ij})s_B(r_{ik}) \f]

In this expression, the sum runs over all the atoms that were specified using the BRIDGING_ATOMS keyword, $s_A$ and $s_B$ are switching functions, and $r_{ij}$ and $r_{ik}$ are the distances between atom $i$ and $j$ and between atoms $i$ and $k$. Less formally, this formula ensures that $j,k$ element of the output matrix is one if there is a bridging atom between atom $j$ and $k$.

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

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 a matrix with elements equal to one if there is a bridging atom between the two atoms 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 all the elements in the input matrix: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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

References

More information about how this action can be used is available in the following articles: - G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017)

Syntax

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