tmd_pca.dat

# creates a CV that measures the RMSD from a reference pdb structure
# the RMSD is measured after OPTIMAL alignment with the target structure
PCAVARS REFERENCE=plumed_pca_1.pdb TYPE=OPTIMAL LABEL=pca1
PCAVARS REFERENCE=plumed_pca_2.pdb TYPE=OPTIMAL LABEL=pca2
#PCAVARS REFERENCE=plumed_pca_3.pdb TYPE=OPTIMAL LABEL=pca3

DISTANCE ATOMS=1961,1773 LABEL=d1
salt_bridge: ...

MOVINGRESTRAINT
ARG=d1 
AT0=0.35 STEP0=0 KAPPA0=1046  
AT1=0.35 STEP1=25000000 KAPPA1=1046
AT2=0.35 STEP2=37500000 KAPPA2=0
...

# the movingrestraint
restraint: ...
MOVINGRESTRAINT
ARG=pca1.eig-1,pca2.eig-1
AT0=0.0,0.0 STEP0=0       KAPPA0=0,0
AT1=0.0,0.0        STEP1=1250000       KAPPA1=200000000,200000000
AT2=0.0191,0.0233 STEP2=3750000 KAPPA2=200000000,200000000
AT3=0.0191,0.0233 STEP3=16250000 KAPPA3=200000000,200000000
AT4=0.0191,0.0233 STEP4=20000000 KAPPA4=0,0
...
# monitor the two variables and various restraint outputs
PRINT STRIDE=5000 ARG=pca1.eig-1,pca2.eig-1 FILE=COLVAR