From: Sofya Lushchekina (burunduk_at_gmail.com)
Date: Mon May 05 2014 - 09:32:11 CDT
Dear NAMD experts,
I have a problem with *targetEquilSteps *keyword in colvars file, according
to UG it should be in harmonic context (
http://www.ks.uiuc.edu/Research/namd/cvs/ug/node58.html#22213), following
error appears (NAMD 2.9 Linux and Windows versions tested):
colvars: Error: keyword "targetequilsteps" is not supported, or not
recognized in this context.
without this keyword run starts normally, output suggests, that
targetEquilSteps is not supposed in colvars at all (see below). Any ideas
how to enable discarding of equilibrating steps?
Thank you in advance,
Sofya
colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 500
colvars: # colvarsRestartFrequency = 500
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be
"smdus.restart.colvars.state".
colvars: The final output state file will be "smdus.colvars.state".
colvars: The trajectory file will be "smdus.colvars.traj".
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = r
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass =
14.007.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass =
14.007.
colvars: All components initialized.
colvars: # width = 0.1
colvars: # lowerBoundary = 18.1
colvars: # lowerWallConstant = 100
colvars: # lowerWall = 18.1 [default]
colvars: # upperBoundary = 18.5
colvars: # upperWallConstant = 100
colvars: # upperWall = 18.5 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = on
colvars: Enabling the extended Lagrangian term for colvar "r".
colvars: # extendedTemp = 300 [default]
colvars: # extendedFluctuation = 0.02 [default]
colvars: Computed extended system force constant: 1490.39 kcal/mol/U^2
colvars: # extendedTimeConstant = 80 [default]
colvars: Computed fictitious mass: 241613 kcal/mol/(U/fs)^2 (U: colvar
unit)
colvars: # outputEnergy = off [default]
colvars: # extendedLangevinDamping = 0 [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars:
----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "harmonic1" [default]
colvars: # colvars = { r }
colvars: # forceConstant = 5
colvars: The force constant for colvar "r" will be rescaled to 500
according to the specified width.
colvars: # centers = { 18.1 }
colvars: # targetCenters = { 18.5 }
colvars: # targetForceConstant = 0 [default]
colvars: # targetNumSteps = 200000
colvars: # targetNumStages = 0 [default]
colvars: # targetForceExponent = 1 [default]
colvars:
----------------------------------------------------------------------
colvars: Initializing a new "histogram" instance.
colvars: # name = "histogram1" [default]
colvars: # colvars = { r }
colvars: # outputfreq = 1000
colvars: Histogram will be written to file smdus.histogram1.dat
colvars: Finished histogram setup.
colvars:
----------------------------------------------------------------------
colvars: Collective variables biases initialized, 2 in total.
colvars:
----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars:
----------------------------------------------------------------------
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