Re: DCOLVARS_DEBUG

From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Tue May 05 2009 - 10:17:43 CDT

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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