From: Chris Harrison (charris5_at_gmail.com)
Date: Sat Mar 12 2011 - 20:52:30 CST
Axel's right. The correct commands are "lowerBoundary" and
"upperBoundary". Not sure if the documentation reflects this (if
not let us know), but these are the commands in the code.
Best,
Chris
--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu Voice: 217-244-1733
http://www.ks.uiuc.edu/~char Fax: 217-244-6078
Axel Kohlmeyer <akohlmey_at_gmail.com> writes:
> Date: Sat, 12 Mar 2011 17:02:38 -0500
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: Francesco Pietra <chiendarret_at_gmail.com>
> Cc: NAMD <namd-l_at_ks.uiuc.edu>
> Subject: Re: namd-l: Keyword "lower" not supported...colvars
>
> 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.
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:55 CST