ABF error on NAMD 2.10

From: Haleh a (halehabdi_at_sabanciuniv.edu)
Date: Mon Nov 02 2015 - 05:55:59 CST

Dear NAMD users,

Recently, I have been trying to run ABF simulations with RMSD as the
collective variables. I am using the following *.in file:

#rmsd.in
Colvarstrajfrequency 1000
Colvarsrestartfrequency 1000
colvar {
name RMSD
width 0.05
lowerboundary 0.1
upperboundary 1.25
lowerwallconstant 100.0
upperwallconstant 100.0
outputAppliedForce on

rmsd {
atoms {
psfSegID P1
atomNameResidueRange CA 1-159
atomsFile main_abf.pdb
atomsCol B
atomsColValue 1.0
}
refPositionsFile ref_abf.pdb
refPositionsCol B
refPositionsColValue 1.0
}
}

abf {
colvars RMSD
fullSamples 1000
}

I am getting the following error on NAMD 2.10 on a cluster :

colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 1000
colvars: # colvarsRestartFrequency = 1000
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "abf.colvars.state".
colvars: The final output state file will be "abfo.colvars.state".
colvars: The trajectory file will be "abfo.colvars.traj".
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = RMSD
colvars: Initializing a new "rmsd" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: Error: definition for atom group "atoms" not found.
colvars: If this error message is unclear, try recompiling with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.

I tried running the same script on NAMD 2.9 on my desktop. It does not give
me the same error. However, my Abf.colvar.state and abf.pmf files are empty
as follows:

 abf.pmf file:

  xi A(xi)
       0.1 0
      0.15 0
       0.2 0
      0.25 0
       0.3 0
      0.35 0
       0.4 0
      0.45 0
       0.5 0
      0.55 0
       0.6 0
      0.65 0
       0.7 0
      0.75 0
       0.8 0
      0.85 0
       0.9 0
      0.95 0
         1 0
      1.05 0
       1.1 0
      1.15 0
       1.2 0
      1.25 0

and

Abf.colvar.state

configuration {
  step 1104000
  dt 1.00000000000000e+000
}

colvar {
  name RMSD
  x 1.56341258634097e+000
}

abf {
  configuration {
    name abf1
  }
samples
 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0

gradient
 0 0 0
 0 0 0
 0 0 0
 0 0 0
 0 0 0
 0 0 0
 0 0 0
 0 0
}

Any suggestion to remove the error and help me get more clear on the
subject is highly appreciated.

Best regards,
Haleh

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