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| 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.
| 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 |
| 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 parallelize |
| 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 |
The following example instructs plumed to calculate the number of water molecules that are bridging betweeen atoms 1-10 and atoms 11-20 and to print the value to a file
BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 LABEL=w1 PRINT ARG=a1.mean FILE=colvar
1.8.14