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colvars configuration well-tempered metadynamics
# 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
}
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