3d_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. 
 
 metad: METAD ARG=pca1.eig-1,pca2.eig-1,pca3.eig-1 PACE=500 HEIGHT=100 SIGMA=10,10 GRID_MIN=-40,-40,-40 GRID_MAX=40,40,40 GRID_SPACING=0.05,0.05,0.05 GRID_WSTRIDE=10000 GRID_RFILE=GRIDS GRID_WFILE=GRIDS


 # monitor the two variables and the metadynamics bias potential
 PRINT STRIDE=10 ARG=pca1.eig-1,pca2.eig-1,pca3.eig-1,metad.bias FILE=COLVAR