Defining colvars groups of atoms for ABF

From: Maria Pikoula (maria.pikoula_at_pmb.ox.ac.uk)
Date: Wed Aug 21 2013 - 04:13:57 CDT

Hello all,

It's my first time trying out this feature and I mainly based my configuration files on relevant tutorials. The reaction coordinate is simply the distance between two atoms but apparently I'm not doing it right, so I get this error:

colvars: Initializing a new collective variable.
colvars: # name = AtomDistance
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: Error: definition for atom group "group1" not found.
colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
---------------
Below I copy the input file for colvars:

colvarsTrajFrequency 2000
colvarsRestartFrequency 20000
colvar {
   name AtomDistance
width 0.1
   lowerboundary 5.0
   upperboundary 45.0
   lowerwallconstant 10.0
   upperwallconstant 10.0
   distance {
      group1 {
         atomNumbers {
            69
        }
      }
      group2 {
         atomNumbers {
            221
        }
} }
}
abf {
   colvars AtomDistance
   fullSamples 500
   hideJacobian
}

Any help is very much appreciated

Cheers,

Maria

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