Whenever you have a multicolvar action such as:

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

COORDINATIONNUMBER SPECIESthis keyword is used for colvars such as coordination number. =1-100 SWITCHthe switching function that it used in the construction of the contact matrix ={RATIONAL R_0=1. D_MAX=3.0}  MORE_THANcalculate the number of variables that are more than a certain target value. ={RATIONAL R_0=6.0 NN=6 MM=12 D_0=0}  The COORDINATIONNUMBER action with label

@0_grp: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =1-100 The GROUP action with label @0_grp defines a group of atoms so that they can be referred to later in the input
@0_mat: CONTACT_MATRIX GROUPspecifies the list of atoms that should be assumed indistinguishable. =1-100 SWITCHspecify the switching function to use between two sets of indistinguishable atoms.
=RATIONAL,R_0=1.,D_MAX=3.0 The CONTACT_MATRIX action with label @0_matYou 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.