Fwd: Keyword "lower" not supported...colvars

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Mar 13 2011 - 05:37:41 CDT

Distraction again. When the minimization is for all atoms, protein
included, heating has no problems.
francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sun, Mar 13, 2011 at 8:11 AM
Subject: Re: namd-l: Keyword "lower" not supported...colvars
To: Chris Harrison <charris5_at_gmail.com>

Hi Axel & Chris: The error in colvars was pedestrian indeed. The
documentation is correct and the error message should have been taken
literally as it was.

There was another error in the colvars .in file

 colvars colvar1 colvar2 colvar3 colvar4 colvar5
 colvar6 colvar7 colvar8 colvar9

lacking { ....}, so that colvar6 was not recognized.

Now it runs, though two H atoms not involved in colvars are "moving
too fast" at the first stepwise heating from 0.5 to 1 K. I thought
from the good gradient that minimization was perfect, while the
periodicity looked like in order. On looking at the minimization log,
vdw is high:

ETITLE:      TS           BOND          ANGLE          DIHED
IMPRP               ELECT            VDW       BOUNDARY           MISC
       KINETIC               TOTAL           TEMP      POTENTIAL
  TOTAL3        TEMPAVG            PRESSURE      GPRESSURE
VOLUME       PRESSAVG      GPRESSAVG

ENERGY:    5000     37136.3158     27065.2949      6732.8955
73.0007       -1053617.2231    175046.1917         0.0000
0.0000         0.0000        -807563.5244         0.0000
-807563.5244   -807563.5244         0.0000          -4298.3367
-4299.2972   2362522.6570     -4298.3367     -4299.2972

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 5000
WRITING COORDINATES TO RESTART FILE AT STEP 5000
FINISHED WRITING RESTART COORDINATES
The last position output (seq=5000) takes 0.065 seconds, 438.821 MB of
memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 5000
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=5000) takes 0.021 seconds, 438.094 MB of
memory in use
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 5000
WRITING COORDINATES TO OUTPUT FILE AT STEP 5000
The last position output (seq=-2) takes 1.227 seconds, 439.311 MB of
memory in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP 5000
The last velocity output (seq=-2) takes 0.811 seconds, 438.561 MB of
memory in use

Charmrun> Graceful exit.

thanks
francesco

On Sun, Mar 13, 2011 at 3:52 AM, Chris Harrison <charris5_at_gmail.com> wrote:
> 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 : Wed Feb 29 2012 - 05:23:40 CST