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}  The BRIDGE action with label w1 calculates a single scalar value
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 The PRINT action with label

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