d1: READ FILE=plumed.in VALUES=c1
d2: READ FILE=plumed.in VALUES=c2
d3: READ FILE=plumed.in VALUES=c3

ff: COLLECT_FRAMES ARG=d1,d2,d3
oo: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=ff
ll: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=oo NLANDMARKS=250

CLASSICAL_MDS ...
  USE_OUTPUT_DATA_FROM=ll
  NLOW_DIM=2
  LABEL=mds
... CLASSICAL_MDS

SKETCHMAP_CONJGRAD ...
  USE_OUTPUT_DATA_FROM=mds
  HIGH_DIM_FUNCTION={SMAP R_0=4 A=3 B=2}
  LOW_DIM_FUNCTION={SMAP R_0=4 A=1 B=2}
  CGTOL=1E-4 LABEL=smap
... SKETCHMAP_CONJGRAD

pp: PROJECT_ALL_ANALYSIS_DATA PROJECTION=smap USE_OUTPUT_DATA_FROM=oo CGTOL=1E-3
OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=pp FMT=%8.2f ARG=pp.* FILE=projections 
