From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Mar 12 2011 - 16:02:38 CST
just look at the output!
even without looking at the documentation, i would
say that "lower boundary" looks suspiciously like the
root of the problem. i would try "lowerboundary" (one word) instead.
axel.
On Sat, Mar 12, 2011 at 12:16 PM, Francesco Pietra
<chiendarret_at_gmail.com> wrote:
> Hello:
> As a beginner with colvars, probably I am posting pedestrian errors,
> however I was unable to come out. I am trying (namd 2.8 Linux64) to
> heat a protein in a membrane with harmonic restraints on chloride
> anions pertaining to the protein. The .log relative to colvars reads:
>
> Info: CREATING 13890 COMPUTE OBJECTS
> Info: useSync: 1 useProxySync: 0
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> Info: NONBONDED TABLE SIZE: 769 POINTS
> colvars: ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 2011-01-03.
> colvars: # analysis = off [default]
> colvars: # colvarsTrajFrequency = 100
> colvars: # colvarsRestartFrequency = 200
> colvars: # colvarsTrajAppend = off [default]
> colvars: The restart output state file will be "./heat.restart.colvars.state".
> colvars: The final output state file will be "./heat.colvars.state".
> colvars: The trajectory file will be "./heat.colvars.traj".
> colvars: ----------------------------------------------------------------------
> colvars: Initializing a new collective variable.
> colvars: # name = colvar1
> 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: Atom group "group1" defined, 1 initialized: total mass = 35.45.
> colvars: Initializing atom group "group2".
> colvars: Atom group "group2" defined, 2 initialized: total mass = 28.014.
> colvars: All components initialized.
> colvars: # width = 1
> colvars: # lowerBoundary = 0 [default]
> colvars: # lowerWallConstant = 100
> colvars: # lowerWall = -5
> colvars: # upperBoundary = 10
> colvars: # upperWallConstant = 100
> colvars: # upperWall = 5
> colvars: # expandBoundaries = off [default]
> colvars: # extendedLagrangian = off [default]
> colvars: # outputValue = on [default]
> colvars: # outputVelocity = off [default]
> colvars: # outputSystemForce = on
> colvars: # outputAppliedForce = off [default]
> colvars: Error: keyword "lower" 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.
>
> ____________________________
> Below, an excerpt from the colvars .in file (inserted into the namd
> the .conf file) showing the first colvar block and the harmonic block.
> The other eight colvar
> blocks have identical layout:
>
> colvarsTrajFrequency 100 # output values every 100 steps (default)
> colvarsRestartFrequency 200 # must be > colvarsTrajFrequency
>
> colvar {
> name colvar1 # needed to identify the variable
>
> width 1.0 # twice the standard deviation during
> # very short simulation; default 1.0
>
> lower boundary -10.0
> upperboundary 10.0
>
> lowerWall -5.0 # a lttle higher than lowerBoundary
> upperWall 5.0 # a little lower than upperBoundary
>
> lowerWallConstant 100.0 # force constant in kcal/mol
> upperWallconstant 100.0
>
> outputSystemForce yes # reports also the system force on this
> # colvar in addition to the current value
>
> distance {
> group1 {
> atomNumbers 6763 # CLA427A(O1)
> }
> group2 {
> atomNumbers 4327 4324 # NH1 NE of ARG273A(P1)
> }
> }
> }
>
> .......................................
>
> harmonic {
>
> name CLA_harmonic
>
> colvars colvar1 colvar2 colvar3 colvar4 colvar5
> colvar6 colvar7 colvar8 colvar9
>
> centers 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>
> forceConstant 100.0
> }
>
>
> Thanks for help
>
> francesco pietra
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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