From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon May 05 2014 - 10:01:03 CDT
Dear Sofya,
Indeed, that option is a recent addition, yet NAMD 2.9 is now somewhat old, and contains an older version of the colvars module (as it says in the output: 2012-03-23). You can get an updated version either by downloading a nightly build of NAMD, or the latest version of the colvars module code (from http://colvars.github.io/) and recompiling NAMD.
Best,
Jerome
----- Original Message -----
> 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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