Definition of two colvars for ABF

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Wed Dec 30 2009 - 14:41:20 CST

Dear All,

I am trying to define two colvars for ABF (2.7b1 Windows version), using
configuration given below, all atoms belong to the same molecule and
atoms in first colvar do not overlapped with the atoms of the second one
(i.e. are orthogonal). Simulation using the first colvars only proceed
smoothly, but the second one is likely the problem. So the question
is are boundaries for "gyration" must be defined, if are requisite how
to estimate values . As a additional note still I can't find
colvars.state file during successfully simulation. Best wishes to
developers and users in New 2010.

Kind regards

Branko

Output (problem underlined):

colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 29-09-2008.
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 10000
colvars: # trajAppend = off [default]
colvars: The restart output state file will be
"C:\namd2\246triEtinthd.restart.colvars.state".
colvars: The trajectory file will be "C:\namd2\246triEtinthd.colvars.traj".
colvars: The final output state file will be
"C:\namd2\246triEtinthd.colvars.state".
colvars: # analysis = on
colvars:
----------------------------------------------------------------------
colvars: # readTrajectory = "" [default]
colvars: # readBegin = 0 [default]
colvars: # readEnd = 0 [default]
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = d
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 3 atoms, total mass = 36.0321.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 3 atoms, total mass = 44.0095.
colvars: All components initialized.
colvars: # width = 0.01
colvars: # lowerBoundary = 3.35
colvars: Lower boundary defined.
colvars: # upperBoundary = 9.7
colvars: Upper boundary defined.
colvars: # lowerWallConstant = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = gyration
colvars: Initializing a new "radius of gyration" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: Initializing atom group "atoms".
colvars: Atom group "atoms" defined, 15 atoms, total mass = 212.181.
colvars: All components initialized.
colvars: # width = 0.01
colvars: # lowerBoundary = 0 [default]
colvars: Lower boundary was not defined.
colvars: # upperBoundary = 0 [default]
colvars: Upper boundary was not defined.
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars:
----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars:
----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { d, gyration }
colvars: # applybias = on
colvars: # hidejacobian = off
colvars: Jacobian (geometric) forces will be included in reported free
energy gradients.
colvars: # fullsamples = 500
colvars: # inputprefix = [default]
colvars: # outputfreq = 1000
colvars: _Tried to initialize a count grid on variable with undefined
boundaries._
colvars: _If this error message is unclear, try recompile with
-DCOLVARS_DEBUG_.
FATAL ERROR: Error in the collective variables module: exiting.

Input:

colvarsTrajFrequency 1
colvarsRestartFrequency 10000
analysis on

colvar {

   name d

   lowerBoundary 3.35
   upperBoundary 9.70
   width 0.01

   distance {
       group1 {
          atomnumbers 1 3 5
       }
       group2 {
          atomnumbers 16 17 18
       }
   }
}

colvar {
   name gyration
   width 0.01

   gyration {
       atoms {
          atomNumbers 7 8 9 10 11 12 13 14 15 19 20 21 22 23 24
       }
     }
}

abf {
   colvars d gyration
   fullSamples 500
   hideJacobian no
   outputFreq 1000
   applyBias yes
}

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