ColVars manual clarification

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1

Hi,
I intend to do a PMF analysis using ColVars (lammps/15May15). I have read ColVars manual, but one part is not clear enough for me.
Regarding the centers and targetCenters, which case is correct (see figure)?
I have tried different cases, but don’t see a certain behavior; The object either does not desorb from the surface, or it jumps from the surface and then smoothly moves to the target point.
Thanks so much.

PMF-ColVars.jpg

ColVars input:

colvarsTrajFrequency 1
colvarsRestartFrequency 1000

colvar {
name Des
width 1
lowerBoundary 0.0
upperBoundary 18.0

force constants

lowerWallConstant 5000
upperWallConstant 5000

hardLowerBoundary on

outputs

outputAppliedForce on

#distanceZ colvar

distanceZ {

main {
atomNumbersRange 1-18 #ring
}
ref {
dummyAtom (9.97907, 10.0362, 1.97266) #ref
}
axis (0,0,1)
}
}

harmonic {
name Desorb-PMF
colvars Des
centers 16.02734 #go from 1.97266 (18 - 1.97266 = 16.02734) forceConstant 100.0 # constant force targetCenters 0.0 #to 18

targetNumSteps 2000

outputEnergy on
outputCenters on
outputAccumulatedWork on
}

2

Hello Xiaolin, if you are using a distance variable, the center of the restraint is not a position in space, but rather the value that the variable should have in order to satisfy the restraint.

Simply put, if you are trying to drag a molecule (group “main” in your example) towards a set position (dummy group “ref”), the value of “center” should be close to the initial distance between main and ref, and “targetCenters” should be zero.

Regarding the “jumps”, keep in mind that while all centers of mass/geometry are calculated as simple weighted sums of vectors, all distances between these centers are calculated using PBCs.

Giacomo

PMF-ColVars.jpg