# structural info
MOLINFO STRUCTURE=structure.pdb

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

# cryo-EM CVs
EMMI ...
LABEL=gmm NO_AVER NOPBC TEMP=300.0 NL_STRIDE=20 NL_CUTOFF=0.001
ATOMS=protein-h GMM_FILE=1ubq_GMM_PLUMED.dat
SIGMA_MIN=0.01 RESOLUTION=0.1 NOISETYPE=GAUSS
WRITE_STRIDE=1000 SIGMA0=0.2 DSIGMA=0.0
...

EMMI ...
LABEL=gmmnd NO_AVER NOPBC TEMP=300.0 NL_STRIDE=20 NL_CUTOFF=0.001
ATOMS=protein-h GMM_FILE=1ubq_GMM_PLUMED.dat
SIGMA_MIN=0.01 RESOLUTION=0.1 NOISETYPE=GAUSS
WRITE_STRIDE=1000 SIGMA0=0.2 DSIGMA=0.0
NUMERICAL_DERIVATIVES
...

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