Metadynamic Electron Microscopy MetaInference (MEMMI)

https://github.com/fbrotzakis/MEMMI

Plumed example: 

PBMETAD ...

   BIASFACTOR=56 HEIGHT=0.3 PACE=200 WALKERS_MPI LABEL=pb GRID_WSTRIDE=10000 SIGMA=1000 ADAPTIVE=DIFF

   ARG=CV1,CV2,CV3

   SIGMA_MIN=value_min1,value_min2,value_min3

   SIGMA_MAX=value_max1,value_max2,value_max3

   GRID_MIN=grid_value_min1,grid_value_min2,grid_value_min3

   GRID_MAX=grid_value_max1,grid_value_max2,grid_value_max3

   FILE=../HILLS_CV1,../HILLS_CV2,../HILLS_CV3

   GRID_WFILES=../GRID_CV1,../GRID_CV2,../GRID_CV3

...

EMMI ...

   ARG=pb.bias REWEIGHT

   LABEL=gmm NOPBC TEMP=310.0 NL_STRIDE=100 NL_CUTOFF=0.01

   ATOMS=protein-h GMM_FILE=../iapp.dat

   # the larger the number the softer the contribution of the EM data

   SIGMA0=5.0 SIGMA_MIN=0.05 DSIGMA=0.1 RESOLUTION=0.42 NOISETYPE=GAUSS

   OPTSIGMAMEAN SIGMA_MEAN0=2.0

   AVERAGING=200 WRITE_STRIDE=10000

...

Dynamically Optimized Collective variables

https://github.com/fbrotzakis/PLUMED2_TICA

AlphaFold-IDP

https://github.com/vendruscolo-lab/AlphaFold-IDP