# structural info
MOLINFO STRUCTURE=structure.pdb

# define all heavy atoms
protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H

# cryo-EM CV
gmm:   EMMI NO_AVER NOPBC SIGMA_MEAN=0.01 TEMP=300.0 NL_STRIDE=1 NL_CUTOFF=0.01 ATOMS=protein-h GMM_FILE=1ubq_GMM_PLUMED.dat 

# printout
DUMPDERIVATIVES ARG=gmm.scoreb STRIDE=1 FILE=deriva FMT=%8.4f
PRINT ARG=gmm.scoreb FILE=COLVAR STRIDE=1
