From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Tue May 05 2009 - 16:19:57 CDT
Hi George, indeed the second error you see is linked to the first, as
I just realized from looking more carefully at the 2.7b1 snapshot,
which I should have done before: sorry I've made you do a redundant
test.
If the atomNumbers version works for you, you can use that, it's
completely equivalent to the atomsFile version. Thank you anyway for
pointing this out!
The cvs tree still contains the same colvars code as 2.7b1. However,
it looks like a synchronization could be useful now...
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 4:29 PM, George Madalin Giambasu
<giambasu_at_gmail.com> wrote:
> 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.
>
> thanks,
>
>
> 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: atomsFile neb01_ii_1.pdb
> 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: 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.
>
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