TOPOLOGY_MATRIX ... 
  NODES=66,17,1 ATOMS=2-16,18-65,67-108 BIN_SIZE=2 
  CYLINDER_SWITCH={RATIONAL R_0=0.1 D_MAX=1} 
  SWITCH={RATIONAL D_0=4 R_0=0.5 D_MAX=10}  
  RADIUS={RATIONAL D_0=0.7 R_0=0.3 D_MAX=3.0} 
  SIGMA=1.0 KERNEL=triangular 
  DENSITY_THRESHOLD={RATIONAL D_0=0.6 R_0=0.2 D_MAX=1.5}
  LABEL=mat
... TOPOLOGY_MATRIX

dfs: DFSCLUSTERING LOWMEM MATRIX=mat 

mm: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM

PRINT ARG=mm.* FILE=colvar FMT=%8.4f
DUMPDERIVATIVES ARG=mm.* FILE=deriv FMT=%8.4f
