ABF vs WTMetaD PMF
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Dear, I am performing the PMF calculation using the ABF method (classic) and tempered metadynamics, but the PMF I obtain are totally different. I am using the distance between monomers of my protein as a collective variable. When I did a test using each alanine, the PMF curves were very similar, but now when I use it for my system (protein dimer), the maximum values of my curve with ABF reach up to 200 kcal/mol while with metadynamics it reaches only up to 40 kcal/mol (more reasonable), reading a little here and some articles, I couldn't find a clear reason for what I'm observing, maybe you can help me direct these results.
colvar common to both methods.
colvarsTrajFrequency 500
colvarsRestartFrequency 500
colvar {
name AtomDistance
width 0.10 # Mesmo do que CHARMM-GUI and também BFEE2. Não considere lower/upperWall.
lowerboundary 53.6 # O valor é zero, porque a diferencia de distanciaentre os dímeros é 0.0.
upperboundary 103.6 # O valor máximo para evaluar o PMF.
expandboundaries on
distance {
forceNoPBC yes
group1 {
atomsFile P1.pdb # PROA ou PROC.
atomsCol B
atomsColValue 1.0
}
group2 {
atomsFile P2.pdb # PROB.
atomsCol B
atomsColValue 1.0
}
}
}
harmonicWalls {
name ABF-Walls
colvars AtomDistance
lowerWalls 53.6 # lowerboundary.
upperWalls 103.6 # upperboundary.
lowerWallConstant 10.0 # Força mesma como em charmm-gui.
upperWallConstant 10.0 # Força mesma como em charmm-gui.
}
´´´
setting for ABF
```bash
abf {
name ABF-Distance
colvars AtomDistance
fullSamples 10000
hideJacobian # Exclui a entropia geométrica. so para distance e distanceXY.
# fonte: https://github.com/Colvars/colvars/issues/367
historyfreq 500 # Salva o free energy gradient, sampling histograma e PMF no mesmo arquivo.
}
´´´
setting for metadynamics
```bash
metadynamics {
name WTMetaD-Distance
colvars AtomDistance
hillWeight 0.25
newHillFrequency 500 # Valor padrão.
hillwidth 0.5
writeHillsTrajectory on # Escreve un arquivo para armazenar os Hills (kcal/mol)
wellTempered on # Favorece WellTempered Metadynamics.
biasTemperature 4340 # O Bias factor é calculado como:
# biasFactor = (TemperatureMD + biasTemperature) / TemperatureMD
# Onde TemperatureMD é a temperatura escolhida da simulação.
# e biasTemperature é a temperatura escolhida aquí, na metadinâmica, biasFactor 15 cá.
}
´´´
Hi, this sounds like a convergence issue, highly system-specific. To diagnose it I would compare the colvar trajectories for the two methods, and then the molecular trajectories in general. Something must be behaving qualitatively differently.
Side note: the hideJacobian option gives an ABF-specific type of free energy profile that is not equal to that given by metadynamics. I doubt this is the source of error here. In doubt, don't use hideJacobian.