From: Takeru KAMEDA (kamedapon_at_hiroshima-u.ac.jp)
Date: Sun Sep 29 2019 - 21:19:47 CDT
Dear all.
Hi. I am trying multi-canonical ensemble method using NAMD2.13.
I wrote colvar file as follows:
colvarsTrajFrequency 5000
colvarsRestartFrequency 50000
colvar {
name theta
outputValue on
#outputVelocity on
#outputEnergy on
#outputSystemForce on
#outputAppliedForce on
orientation {
atoms { atomnumbers {
13754 13755 13756 13757 13758 13761 13783 13785 19290 19291 19292 19293 19294 19297 19319 19321
}}
refPositionsFile ./colvar.pdb
refPositionsCol O
}
}
abf {
colvars theta
fullSamples 200
hideJacobian
}
Then, we execute simulation, following error was output:
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-10-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using NAMD interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "colvar.in":
colvars: # smp = on [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 5000
colvars: # colvarsRestartFrequency = 50000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "theta"
colvars: Initializing a new "orientation" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "atoms".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "atoms" defined, 16 atoms initialized: total mass = 195.991, total charge = -1.86.
colvars: # refPositions = [default]
colvars: # refPositionsFile = "./colvar.pdb"
colvars: # refPositionsCol = "O"
colvars: # refPositionsColValue = 0 [default]
Info: Found 351 unique exclusion lists needing 1152 bytes
Info: Found 351 unique exclusion lists needing 1152 bytes
Info: Found 351 unique exclusion lists needing 1152 bytes
Info: Found 351 unique exclusion lists needing 1152 bytes
colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry.
colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { theta }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: Static feature "scalar" may not be enabled as a dependency in colvar theta.
colvars: ...required by "require scalar variables" in bias abf1
colvars: Error: Failed dependency in bias abf1.
FATAL ERROR: Error in the collective variables module: exiting.
Any parts of configulation file was wrong?
Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan
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