dist: DISTANCE ATOMS=1,2 

ff1: COLLECT_FRAMES ATOMS=1-5 STRIDE=1 
ss1: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=ff1 

ff2: COLLECT_FRAMES ARG=dist STRIDE=1 
ss2: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=ff2 

l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=2
l2: RESELECT_LANDMARKS USE_OUTPUT_DATA_FROM=ss2 LANDMARKS=l1 

OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=l2 FILE=data FMT=%8.4f
PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=l2 FILE=mymatrix.dat FMT=%8.4f
