From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Tue May 05 2009 - 13:53:18 CDT
Hi George, if only the atoms of group1 have an occupancy different
than zero, you don't need to specify atomsColValue, or even atomsCol
for that matter. In the source code that comes with 2.7b1, there is a
bug that gives this kind of error if you use atomsColValue when not
really required. This bug has been fixed in the code that will go
into 2.7, of course.
Removing atomsColValue should work, otherwise let us know.
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 11:17 AM, George Madalin Giambasu
<giambasu_at_gmail.com> wrote:
>
> HI Jerome,
>
> thanks, I made the change and got namd compiled. I still get an error I
> can't understand when defining group1 of a distance colvar by reading
> the beta field of a pdb file (bellow). The pdb file has the same number
> of atoms as the topology (amber) and the beta field modifications were
> done with vmd.
>
>
> Any clue? Is there anything special about the format of the pdb file?
>
>
> 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: atomsFile neb01_ii_1.pdb
> colvars: atomsCol B
> colvars: atomsColValue 1.00
> 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: Error: no atoms defined for atom group "group1".
> 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 is how I set up the colvar:
>
> colvar {
> name rmsd_0
> lowerBoundary 2.0
> lowerWallConstant 30.0
> upperBoundary 3.0
> upperWallConstant 30.0
> outputValue on
> outputSystemForce on
> outputAppliedForce on
>
> distance {
>
> group1 {
> atomsFile /usr/people/madu/workspace/colvars_test/neb01_ii_1.pdb
> atomsCol B
> atomsColValue 1.00
> }
>
> group2 {
> dummyAtom ( 0.0,0.0,0.0 )
> }
>
> onesiteSystemForce yes
> componentCoeff 1.0
> }
>
>
>
>
>
>
>
> Jerome Henin wrote:
>> Hi George,
>>
>> In the Makefile, you can add this flag to the variable EXTRADEFINES.
>>
>> Best,
>> Jerome
>>
>> On Mon, May 4, 2009 at 11:49 PM, George Madalin Giambasu
>> <giambasu_at_gmail.com> wrote:
>>
>>> Hi,
>>>
>>>
>>> where should the -DCOLVARS_DEBUG option be added for namd2.7 compilation?
>>>
>>>
>>> thanks in advance,
>>>
>>> g.
>>>
>>>
>>>
>
>
> --
> ________________________________________________________________________
> George Madalin Giambasu PhD Student
> University of Minnesota Phone : (612) 625-6317
> Department of Chemistry Fax : (612) 626-7541
> 207 Pleasant St. SE e-mail:
> Minneapolis, MN USA 55455-0431 GeorgeMGiambasu_at_umn.edu
> York Research Group giambasu_at_gmail.com
> http://theory.chem.umn.edu/
> ________________________________________________________________________
>
>
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