colvars configuration well-tempered metadynamics

gistfile1.txt

# 12th Sept 2018
# META - 01 - NAMD/colvars
#
# Well-Tempered metadynamics + harmonic restraints
# CV1 : Distance projected in the difussion axis
# CV2 : Distance projected in the orthogonal plane of difussion axis
# WT-Metadyn(CV1)
# Harmonic(CV2)
#
#----------------------------------------------------------------------------- #
# colvars save freq
# ---------------------------------------------------------------------------- #
colvarstrajfrequency 500
colvarsrestartfrequency 3000
#colvarsInput ligA_bb_md.colvars.state
#----------------------------------------------------------------------------- #
# CV 1 - Distance on difussion axis# Distance between ligand coordinates during simulation and original
# coordinates, using a roto-translated frame of reference to remove
# the bias of tumbling and difussion of protein-ligand complex.
#
# original positions were calculated using prody over ligA_bb_w.pdb
# X0 = -1.768 0.768 0.765
# Z-axis = 0.332 0.898 -0.288
# ---------------------------------------------------------------------------- #
colvar {
    name DistanceZ
    lowerboundary -10.0
    upperboundary  10.0
    width 0.1
    distanceZ {
        main {
                atomsFile ../input/reference.pdb
                atomscol O
                atomscolvalue 2.0
                centerreference on
                rotatereference on
                refpositionsfile ../input/reference.pdb
                fittinggroup {
                    atomsfile ../input/reference.pdb
                    atomscol O
                    atomscolvalue 1.0
                }

        }
        ref {
            dummyatom {
                (-0.009, 0.950, 0.936)
            }
       }
        axis {
            (0.332, 0.898, -0.288)
        }
    }
}
#----------------------------------------------------------------------------- #
# CV 2 - Normal distance to difussion axis
# This variable has as purpose to avoid the difussion of the ligand in the
# solvent.
#
# X0 = 0.332, 0.898, -0.288
# Z-axis 0.332 0.898 -0.288
# ---------------------------------------------------------------------------- #
colvar {
    name DistanceXY
    expandboundaries on
    width 0.1
    lowerBoundary 0.0
    upperBoundary 5.0
    distanceXY {
        main {
                atomsfile ../input/reference.pdb
                atomscol O
                atomscolvalue 2.0
                centerreference on
                rotatereference on
                refpositionsfile ../input/reference.pdb
                fittinggroup {
                    atomsfile ../input/reference.pdb
                    atomscol O
                    atomscolvalue 1.0
                }
        }
        ref {
            dummyAtom {
                (-0.09, 0.950, 0.936)
                }
        }
        axis {
            (0.332, 0.898, -0.288)
        }
    }
}
#----------------------------------------------------------------------------- #
# WT-Metadynmics configuration
# DeltaT = 3000
# A = 0.1 kcal
# delta = 0.16 (colvarsu**2)
# ---------------------------------------------------------------------------- #
metadynamics {
    name                     meta_04_wtmetad
    colvars                  DistanceZ
    hillweight               0.1
    hillwidth                0.16
    newHillfrequency         500
    dumpfreeenergyfile       yes
    writehillstrajectory     on
}
harmonicWalls {
    name ha
    colvars DistanceXY
    lowerwalls 0.0
    upperwalls 5.0
    lowerwallconstant 5.0
    upperwallconstant 5.0
}