From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Tue May 05 2009 - 16:46:59 CDT
Hi Giacomo,
please let me know when you synchronize CVS with the colvars module.
In the mean time I discovered smth else :) . When I turn on the
rotateReference option and define a refPositionsGroup which is different
from group1 of the distance, I get the following error (see bellow). The
errors go away only when the two groups are identical.
Thanks again,
George
colvars:
----------------------------------------------------------------------
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
"output.restart.colvars.state".
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:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = rmsd_0
colvars: Initializing a new "distance" component, with configuration:
colvars:
colvars:
colvars: group1 {
colvars: atomnumbers {
colvars: 12 14 16
colvars: }
colvars: centerReference on
colvars: refPositionsGroup {
colvars: atomnumbers {
colvars: 11 12 14
colvars: }
colvars: }
colvars: refPositions {( -7.156, -1.177 ,-11.151 )( -6.480, -2.353
,-10.892 )( -6.730, -3.065 , -9.760 )( -7.703, -2.623 , -8.786 )}
colvars:
colvars: }
colvars: group2 {
colvars: dummyAtom ( 0.0,0.0,0.0 )
colvars: }
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: Requesting atom 12 for collective variables calculation.
colvars: The index of this atom in the colvarproxy_namd arrays is 0.
colvars: Requesting atom 14 for collective variables calculation.
colvars: The index of this atom in the colvarproxy_namd arrays is 1.
colvars: Requesting atom 16 for collective variables calculation.
colvars: The index of this atom in the colvarproxy_namd arrays is 2.
colvars: Within atom group "group1":
colvars: Defining atom group "refPositionsGroup".
colvars: Initializing atom group "refPositionsGroup".
colvars: Requesting atom 11 for collective variables calculation.
colvars: The index of this atom in the colvarproxy_namd arrays is 3.
colvars: Requesting atom 12 for collective variables calculation.
colvars: The index of this atom in the colvarproxy_namd arrays is 0.
colvars: Requesting atom 14 for collective variables calculation.
colvars: The index of this atom in the colvarproxy_namd arrays is 1.
colvars: Done initializing atom group with name "refPositionsGroup".
colvars: Checking the validity of "atomnumbers".
colvars: Atom group "refPositionsGroup" defined, 3 atoms, total
mass = 38.03.
colvars: Using reference positions from input file.
colvars: Error: reference positions for "group1" do not match the
number of atom indexes.
FATAL ERROR: Error in the collective variables module: exiting.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
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