From: George Madalin Giambasu (
Date: Tue May 05 2009 - 15:29:43 CDT

Hi again,

Unfortunately I still get an error (different) when omitting atomsCol
and atomsColValue (see bellow).
Now, if I specify group1 as an atomNumbers list (the exact list that has
the O and B positive), the errors disappear.

I am using last week's namd cvs version.

I'll be glad to make further testing.



colvars: Initializing the collective variables module, version 29-09-2008.
colvars: # colvarsTrajFrequency = 100 [default]
colvars: # colvarsRestartFrequency = 500 [default]
colvars: # trajAppend = off [default]
colvars: The restart output state file will be
colvars: The trajectory file will be "output.colvars.traj".
colvars: The final output state file will be "output.colvars.state".
colvars: # analysis = off [default]
colvars: Initializing the collective variables.
colvars: Initializing a new collective variable.
colvars: # name = rmsd_0
colvars: Initializing a new "distance" component, with configuration:
colvars: group1 {
colvars: atomsFile neb01_ii_1.pdb
colvars: }
colvars: group2 {
colvars: dummyAtom ( 0.0,0.0,0.0 )
colvars: }
colvars: onesiteSystemForce yes
colvars: componentCoeff 1.0
colvars: Initializing cvc base object.
colvars: # componentCoeff = 1
colvars: # componentExp = 1 [default]
colvars: Done initializing cvc base object.
colvars: # oneSiteSystemForce = on
colvars: Computing system force on group 1 only
colvars: Initializing atom group "group1".
colvars: Error: atomsColValue, if provided, must be non-zero.
FATAL ERROR: Error in the collective variables module: exiting.

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:44 CST