From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Apr 15 2011 - 11:02:03 CDT
Hello Han, can you send me (in private) the colvars configuration file as an
attachment? There may an issue with the carriage return in the Windows text
file, but in that case the parser should stop with an error sooner than it
does for you.
Also, did you paste the entire file in the email? A closing brace appears
to be missing at the end of the abf block.
Giacomo
---- ----
Giacomo Fiorin - Postdoctoral Researcher
ICMS - Institute for Computational Molecular Science - Temple University
1900 N 12 th Street, Philadelphia, PA 19122
giacomo.fiorin_at_temple.edu
---- ----
On Fri, Apr 15, 2011 at 10:14 AM, Shen, Han <han.shen_at_bme.gatech.edu> wrote:
> Hi all,
> I have a problem in colvars. The same program run well on my computer which
> is Windows. However, when I run the same thing on the supercomputer which is
> Linux, the error happened every time, said: Error: keyword "group1" is not
> supported, or not recognized in this context. Distance.in and log file are
> attached bellow. Would you please help me to take a look and give me some
> suggestions? Thanks in advance!
>
>
> *******************************************************************************
>
> *******************************************************************************
> Distance.in
>
> colvarsTrajFrequency 2000
> colvarsRestartFrequency 20000
>
> colvar {
> name AtomDistance
>
> width 0.1
>
> lowerboundary 8.0
> upperboundary 15.0
>
> lowerwallconstant 10.0
> upperwallconstant 0.2
>
> distance {
> group1 {
> atomnumbers { 1 5 7 }
> }
> group2 {
> atomnumbers { 342 344 346 }
> }
> }
> }
>
>
> abf {
> colvars AtomDistance
> fullSamples 500
> hideJacobian
>
>
> *******************************************************************************
>
> *******************************************************************************
>
> Log file:
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 20091218.
> colvars: # analysis = off [default]
> colvars: # colvarsTrajFrequency = 2000
> colvars: # colvarsRestartFrequency = 20000
> colvars: # colvarsTrajAppend = off [default]
> colvars: The restart output state file will be
> "e3k3b_in.restart.colvars.state".
> colvars: The final output state file will be "e3k3b_in.colvars.state".
> colvars: The trajectory file will be "e3k3b_in.colvars.traj".
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new collective variable.
> colvars: # name = AtomDistance
> colvars: Initializing a new "distance" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # period = 0 [default]
> colvars: # wrapAround = 0 [default]
> colvars: # forceNoPBC = off [default]
> colvars: # oneSiteSystemForce = off [default]
> colvars: Initializing atom group "group1".
> colvars: Error: keyword "" is not supported, or not recognized in
> this context.
> colvars: If this error message is unclear, try recompiling with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
>
> --
> Han Shen
> Wallace H. Coulter Department of Biomedical Engineering
> Georgia Institute of Technology and Emory University
> Room 4165, M Building
> Atlanta, GA 30332
> 770-676-8397
>
>
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