Multicolvar

Whenever you have a multicolvar action such as:

Click on the labels of the actions for more information on what each action computes

COORDINATIONNUMBER 
SPECIES
this keyword is used for colvars such as coordination number. 
=1-100 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching
function defined above. 
={RATIONAL R_0=1. D_MAX=3.0}  
MORE_THAN
calculate the number of variables more than a certain target value. 
={RATIONAL R_0=6.0 NN=6 MM=12 D_0=0}  The COORDINATIONNUMBER action with label 

You will get a colossal speedup by specifying the D_MAX keyword in all switching functions that act on distances. D_MAX tells PLUMED that the switching function is strictly zero if the distance is greater than this value. As a result PLUMED knows that it does not need to calculate these zero terms in what are essentially sums with a very large number of terms. In fact when D_MAX is set PLUMED uses linked lists when calculating these coordination numbers, which is what gives you such a dramatic increase in performance.