From: Ishaan Roy (royi_at_uchicago.edu)
Date: Tue Aug 17 2021 - 15:40:56 CDT
Hello,
I am using eABF on two membrane helices to find the binding energy. During the separation runs, the upper boundary for the distance colvar is set to 40, the distance value only reaches around 20, even when I increase the simulation time. This current maximum it reaches is an inadequate separation, since parts of the proteins are still interacting at this point and the pmf has not levelled off. When looking at the VMD window, there doesn’t seem to be anything obvious that would prevent the ABF from separating them further. Any ideas on what might be going on?
Thanks,
Ishaan
Here are my colvar settings:
#############################################################
## Collective Variables ##
#############################################################
# Global parameters
ColvarsTrajfrequency 20
Colvarsrestartfrequency 100
analysis on
colvar {
name dist
width 0.05
extendedLagrangian on
extendedFluctuation 0.02
outputTotalForce on
lowerboundary 10.0
upperboundary 40.0
distance {
forceNoPBC yes
group1 {
psfSegID PROA
atomNameResidueRange { CA 32-52 }
}
group2 {
psfSegID PROB
atomNameResidueRange { CA 87-106 }
}
}
}
colvar {
name sa1
outputValue off
width 1.0
lowerboundary -180.0
upperboundary 180.0
spinAngle {
atoms {
psfSegID PROA
atomNameResidueRange { CA 32-52}
}
refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb
}
}
colvar {
name sa2
outputValue off
width 1.0
lowerboundary -180.0
upperboundary 180.0
spinAngle {
atoms {
psfSegID PROB
atomNameResidueRange { CA 87-106}
}
refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb
}
}
colvar {
name t1
outputValue off
width 1.0
lowerboundary -1.0
upperboundary 1.0
tilt {
atoms {
psfSegID PROA
atomNameResidueRange { CA 32-52}
}
refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb
}
}
colvar {
name t2
outputValue off
width 1.0
lowerboundary -1.0
upperboundary 1.0
tilt {
atoms {
psfSegID PROB
atomNameResidueRange { CA 87-106}
}
refPositionsFile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb
}
}
colvar {
name RMSD
width 1.0
outputValue off
lowerboundary 0.0
upperboundary 5.0
rmsd {
atoms {
psfSegID PROA PROB
atomNameResidueRange { CA 32-52 }
atomNameResidueRange { CA 87-106}
}
refpositionsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb
}
}
#############################################################
## RESTRAINTS AND PMF
##############################################################
abf {
colvars dist
FullSamples 5000
}
harmonic {
colvars sa1
forceConstant 0.1
centers 0.0
}
harmonic {
colvars sa2
forceConstant 0.1
centers 0.0
}
harmonic {
colvars t1
forceConstant 0.1
centers 1.0
}
harmonic {
colvars t2
forceConstant 0.1
centers 1.0
}
harmonic {
colvars RMSD
forceConstant 10.0
centers 0.0
}
#############################################################
### Restraint on Monomer A
###############################################################
colvar {
name Omega
outputValue off
orientation {
atoms {
psfSegID PROB
atomNameResidueRange { CA 87-106 }
}
refpositionsfile ../c55_kmeans7_darkblue_F3422_solvated_ionized.pdb
}
}
colvar {
name Pin
outputValue off
width 1.0
lowerboundary 22.9
upperboundary 24.9
distance {
group1 {
dummyatom (0, 0, 0)
}
group2 {
psfSegID PROB
atomNameResidueRange { CA 87-106 }
}
}
}
harmonic {
colvars Omega
forceConstant 100.0
centers ( 1.0, 0.0, 0.0, 0.0 )
}
harmonic {
colvars Pin
forceConstant 100.0
centers 23.9
}
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