Tutorial-l Mailing List

From: Ramon Mendoza Uriarte (ramendoza_at_uchicago.edu)
Date: Tue Sep 29 2020 - 18:36:46 CDT

Hello,

I am trying to perform the two-dimensional example that the "One-dimensional replica-exchange umbrella sampling" tutorial specifies. However, whenever I attempt the simulation, I get the following error:

colvars: Initializing a new collective variable.
colvars: # name = "lengtha"
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group1".
colvars: Error: keyword "" is not supported, or not recognized in this context.
FATAL ERROR: Error in the collective variables module: exiting.

I have done a search but have yet to find the solution.
I think these are the relevant code snippets:

from colvars.conf

colvarsTrajFrequency 200

colvar {
  name lengtha
  distance {
    group1 {
      atomNumbers 1
    }
    group2 {
      atomNumbers 30
    }
  }
}

colvar {
  name lengthb
  distance {
    group1 {
      atomNumbers 36
    }
    group2 {
      atomNumbers 66
    }
  }
}

harmonic {
  name lenpot
  colvars lengtha lengthb
  centers 9.0 9.0
  forceConstant 1.0
}

from stretch_alanin.conf

proc replica_bias { i } {
  return [list lenpot "centers [expr 9 + ($i%8)] [expr 9 + ($i/8)]"]
}

Thank you,
Ramon

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