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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.
| ATOMS | the atoms involved in each of the collective variables you wish to calculate. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one CV will be calculated for each ATOM keyword you specify (all ATOM keywords should define the same number of atoms). The eventual number of quantities calculated by this action will depend on what functions of the distribution you choose to calculate. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3... |
| 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