2d_metad_flooding_restart.dat

# restart previous simulation
RESTART

 # set up two variables for Phi and Psi dihedral angles 
 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
 #
 # Activate metadynamics in phi and psi
 # depositing a Gaussian every 500 time steps,
 # with heig-1ht equal to 12 kJoule/mol,
 #  and width 0.35 rad for both CVs. 

UPPER_WALLS ARG=pca1.eig-1 KAPPA=200000000 AT=0.08 LABEL=uwall1
LOWER_WALLS ARG=pca1.eig-1 KAPPA=200000000 AT=-0.08 LABEL=lwall1
                                          
UPPER_WALLS ARG=pca2.eig-1 KAPPA=200000000 AT=0.08 LABEL=uwall2
LOWER_WALLS ARG=pca2.eig-1 KAPPA=200000000 AT=-0.08 LABEL=lwall2
 
 
 metad: METAD ARG=pca1.eig-1,pca2.eig-1 PACE=500 HEIGHT=0.1 SIGMA=0.0005,0.0005 GRID_MIN=-0.1,-0.1 GRID_MAX=0.1,0.1 GRID_SPACING=0.0002,0.0002 GRID_WSTRIDE=10000 GRID_WFILE=GRIDS GRID_RFILE=GRIDS


 # monitor the two variables and the metadynamics bias potential
 PRINT STRIDE=10000 ARG=pca1.eig-1,pca2.eig-1,metad.bias FILE=COLVAR