From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Tue May 05 2009 - 17:14:49 CDT
Yup, you're right: thanks again for taking the time to test that
configuration! We really haven't, because the value of the "distance"
variable is insensitive to rotations, and using rotateReference won't
change your results.
But the code still should allow you to go through your configuration,
because there was nothing wrong with it.
The fix should be relatively easy without CVS, though: can you replace
line 216 in colvaratoms.C with the following two lines?
atom_group *ag = ref_pos_group ? ref_pos_group : this;
if (ref_pos.size() != ag->size()) {
This is for the parsing routine only, the rest of the source file is already ok.
While you're at it, you may also want to remove line 264 (the
select_closest_image() call) which shouldn't be there (it may rise a
bug under very specific circumstances). We've already taken care of
it, but the fix is not yet in the CVS tree, so it's better to get it
out of your way.
Giacomo
---- ----
Giacomo Fiorin
Center for Molecular Modeling at
University of Pennsylvania
231 S 34th Street, Philadelphia, PA 19104-6323
phone: (+1)-215-573-4773
fax: (+1)-215-573-6233
mobile: (+1)-267-324-7676
mail: giacomo.fiorin_<at>_gmail.com
web: http://www.cmm.upenn.edu/
---- ----
On Tue, May 5, 2009 at 5:46 PM, George Madalin Giambasu
<giambasu_at_gmail.com> wrote:
> 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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