BRIDGE
 This is part of the multicolvar 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
w1: BRIDGE BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the
structure. =100-200 GROUPAThe list of atoms that are in the first interesting part of the structure =1-10 GROUPBThe list of atoms that are in the second interesting part of the structure =11-20 SWITCHThe parameters of the two \ref switchingfunction in the above formula ={RATIONAL R_0=0.2}
PRINT ARGthe input for this action is the scalar output from one or more other actions. =w1 FILEthe name of the file on which to output these quantities =colvar

Glossary of keywords and components
The atoms involved can be specified using
 BRIDGING_ATOMS The list of atoms that can form the bridge between the two interesting parts of the structure. GROUPA The list of atoms that are in the first interesting part of the structure GROUPB The list of atoms that are in the second interesting part of the structure
Options
 NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances SERIAL ( default=off ) do the calculation in serial. Do not use MPI LOWMEM ( default=off ) lower the memory requirements TIMINGS ( default=off ) output information on the timings of the various parts of the calculation 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