Re: colvars: Error: Feature unavailable:compute total collective force only from one group center

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Mon Feb 27 2017 - 17:36:53 CST

Unfortunately the test of backwards compatibility with previous colvars input (with the exception of totalForce keyword change) failed.

One might argue that the original colvar input file was not correctly built. The error output is below.

Info: CREATING 5440 COMPUTE OBJECTS
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2017-02-06.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: Using NAMD interface, version 2017-01-09.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "colvarsTrp236ApoAll300nsTripleHillFreq2.12.in":
colvars: # indexFile = "" [default]
colvars: # smp = on [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 500
colvars: # colvarsRestartFrequency = 500
colvars: # colvarsTrajAppend = off [default]
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = on [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "chi1"
colvars: Initializing a new "dihedral" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group1".
colvars: Atom group "group1" defined, 1 atoms initialized: total mass = 14.007, total charge = -0.47.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group2".
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 12.011, total charge = 0.07.
colvars: Initializing atom group "group3".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group3".
colvars: Atom group "group3" defined, 1 atoms initialized: total mass = 12.011, total charge = -0.18.
colvars: Initializing atom group "group4".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group4".
colvars: Atom group "group4" defined, 1 atoms initialized: total mass = 12.011, total charge = -0.03.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = on
colvars: Computing total force on group 1 only
colvars: All components initialized.
colvars: # width = 10
colvars: # lowerBoundary = -180
colvars: Warning: lowerWallConstant and lowerWall are deprecated, please define a harmonicWalls bias instead.
colvars: # lowerWall = -180 [default]
colvars: # upperBoundary = 180
colvars: Warning: upperWallConstant and upperWall are deprecated, please define a harmonicWalls bias instead.
colvars: # upperWall = 180 [default]
colvars: # hardLowerBoundary = off [default]
colvars: # hardUpperBoundary = off [default]
colvars: # expandBoundaries = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = on
colvars: # subtractAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "chi2"
colvars: Initializing a new "dihedral" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group1".
colvars: Atom group "group1" defined, 1 atoms initialized: total mass = 12.011, total charge = 0.07.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group2".
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 12.011, total charge = -0.18.
colvars: Initializing atom group "group3".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group3".
colvars: Atom group "group3" defined, 1 atoms initialized: total mass = 12.011, total charge = -0.03.
colvars: Initializing atom group "group4".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group4".
colvars: Atom group "group4" defined, 1 atoms initialized: total mass = 12.011, total charge = -0.15.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = on
colvars: Computing total force on group 1 only
colvars: All components initialized.
colvars: # width = 10
colvars: # lowerBoundary = -180
colvars: Warning: lowerWallConstant and lowerWall are deprecated, please define a harmonicWalls bias instead.
colvars: # lowerWall = -180 [default]
colvars: # upperBoundary = 180
colvars: Warning: upperWallConstant and upperWall are deprecated, please define a harmonicWalls bias instead.
colvars: # upperWall = 180 [default]
colvars: # hardLowerBoundary = off [default]
colvars: # hardUpperBoundary = off [default]
colvars: # expandBoundaries = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = on
colvars: # subtractAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "metadynamics" instance.
colvars: # name = "metadynamics1" [default]
colvars: # colvars = { chi1, chi2 }
colvars: # outputEnergy = off [default]
colvars: # hillWeight = 0.5
colvars: # newHillFrequency = 3000
colvars: # hillWidth = 2
colvars: Half-widths of the Gaussian hills (sigma's):
colvars: chi1: 10
colvars: chi2: 10
colvars: # multipleReplicas = off [default]
colvars: # useGrids = on [default]
colvars: # gridsUpdateFrequency = 3000 [default]
colvars: # rebinGrids = off [default]
colvars: # keepHills = off [default]
colvars: # writeFreeEnergyFile = on [default]
colvars: # keepFreeEnergyFiles = off [default]
colvars: # writeHillsTrajectory = off [default]
colvars: # wellTempered = off [default]
colvars: # biasTemperature = -1 [default]
colvars: # ebMeta = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: # indexFile = "" [default]
colvars: # smp = on [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 500 [default]
colvars: # colvarsRestartFrequency = 500 [default]
colvars: # colvarsTrajAppend = off [default]
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = on [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonicwalls" instance.
colvars: # name = "chi1lw"
colvars: # colvars = { chi1 }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 20
colvars: # targetForceConstant = 0 [default]
colvars: # lowerWalls = { -180 }
colvars: # upperWalls = { 0 } [default]
colvars: Upper walls were not provided.
colvars: Error: at least one variable is periodic, both walls must be provided .
FATAL ERROR: Error in the collective variables module: exiting.

________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Thursday, February 23, 2017 7:50 PM
To: Bennion, Brian
Cc: namd-l_at_ks.uiuc.edu; Ajasja Ljubetič
Subject: Re: namd-l: colvars: Error: Feature unavailable:compute total collective force only from one group center

Hi Brian, the new harmonicWalls bias indeed replaces the options lowerWall and upperWall, but those will still work.

In general you don't need to use the new syntax if you're continuing an older simulation, Colvars is generally backward-compatible (with a single exception: https://colvars.github.io/totalforce.html).

You are clearly not using the default settings if you are defining lowerWalls explicitly, so please do not state that the default settings are not correct.

Regarding the error, the manual does not need to cover what is explained by the error message. If you apply only a lower wall to an angle, sooner or later the angle will increase beyond +180° and will appear to the left of the lower wall, with an exceedingly high energy.

Giacomo

On Thu, Feb 23, 2017 at 3:58 PM, Bennion, Brian <bennion1_at_llnl.gov<mailto:bennion1_at_llnl.gov>> wrote:
Ok. So it seems that all lower and upperWall forces as well as the constants have been deprecated and replaced with harmonicWalls instances.
The default settings are not correct generated as shown by this error.
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonicwalls" instance.
colvars: # name = "chi1lw"
colvars: # colvars = { chi1 }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 20
colvars: # targetForceConstant = 0 [default]
colvars: # lowerWalls = { -180 }
colvars: # upperWalls = { 0 } [default]
colvars: Upper walls were not provided.
colvars: Error: at least one variable is periodic, both walls must be provided .
FATAL ERROR: Error in the collective variables module: exiting.

This is not described in the namd docs that I can find
Brian

From: Giacomo Fiorin [mailto:giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>]
Sent: Thursday, February 23, 2017 12:44 PM
To: Bennion, Brian <bennion1_at_llnl.gov<mailto:bennion1_at_llnl.gov>>
Cc: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>; Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com<mailto:ajasja.ljubetic_at_gmail.com>>

Subject: Re: namd-l: colvars: Error: Feature unavailable:compute total collective force only from one group center

Hi Brian, you have defined the keywords lower/upper walls, which will confine the variables by half-harmonic potentials, but not the boundaries of the PMF grid (lowerBoundary / upperBoundary).
Giacomo

On Thu, Feb 23, 2017 at 3:35 PM, Bennion, Brian <bennion1_at_llnl.gov<mailto:bennion1_at_llnl.gov>> wrote:
Hello,

I have just recompiled namd2.12 with the cvs nightly from Feb 23.
There have been a number of deprecations that I fixed in my colvar input file. However, one error remains that I have not figure out yet.
Below is my current colvar file. I just wat to map the potential energy surface for two dihedrals of an amino acid in a protein, Chi1 and Chi2.

The error is:
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "metadynamics" instance.
colvars: # name = "metadynamics1" [default]
colvars: # colvars = { chi1, chi2 }
colvars: # outputEnergy = off [default]
colvars: # hillWeight = 0.5
colvars: # newHillFrequency = 3000
colvars: # hillWidth = 2
colvars: Half-widths of the Gaussian hills (sigma's):
colvars: chi1: 10
colvars: chi2: 10
colvars: # multipleReplicas = off [default]
colvars: # useGrids = on [default]
colvars: # gridsUpdateFrequency = 3000 [default]
colvars: # rebinGrids = off [default]
colvars: Feature unavailable: "lower boundary" in colvar chi1
colvars: ...required by "grid" in colvar chi1
colvars: Error: Failed dependency in colvar chi1.
FATAL ERROR: Error in the collective variables module: exiting.
colvarsTrajFrequency 500
colvarsRestartFrequency 500

colvar {
  name chi1
  width 10.0
  lowerWall -180
  upperWall 180
  lowerWallConstant 0.2
  upperWallConstant 0.2
  outputAppliedForce on
  dihedral {
    oneSiteSystemForce
    group1 {
      atomnumbers 3487
    }
    group2 {
      atomnumbers 3489
    }
    group3 {
      atomnumbers 3491
    }
    group4 {
      atomnumbers 3494
    }
  }
}

colvar {
  name chi2
  width 10.0
  lowerWall -180
  upperWall 180
  lowerWallConstant 0.2
  upperWallConstant 0.2
  outputAppliedForce on
  dihedral {
    oneSiteTotalForce
    group1 {
      atomnumbers 3489
    }
    group2 {
      atomnumbers 3491
    }
    group3 {
      atomnumbers 3494
    }
    group4 {
      atomnumbers 3495
    }
  }
}

metadynamics {
  colvars chi1 chi2
  hillWeight 0.5
  hillWidth 2
  newHillFrequency 3000
}

From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] On Behalf Of Bennion, Brian
Sent: Thursday, February 23, 2017 8:39 AM
To: Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>>; NAMD list <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>; Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com<mailto:ajasja.ljubetic_at_gmail.com>>

Subject: Re: namd-l: colvars: Error: Feature unavailable:compute total collective force only from one group center

Thank you both for the info.

I am using the NAMD_CVS-2016-11-11_Source for my build. I will compile a later version.

Brian

________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>>
Sent: Thursday, February 23, 2017 1:10:20 AM
To: NAMD list; Ajasja Ljubetič
Cc: Bennion, Brian
Subject: Re: namd-l: colvars: Error: Feature unavailable:compute total collective force only from one group center

Ajasja pointed correctly to the fix for that bug.
More to that, I believe that the fix is already included in NAMD 2.12: can you try it?
Giacomo

On Thu, Feb 23, 2017 at 2:36 AM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com<mailto:ajasja.ljubetic_at_gmail.com>> wrote:
Hi!
I'm not 100% sure this is related to your problem, but this was on of the larger changes to the colvars module:
https://colvars.github.io/totalforce.html5dCuBZ-92PFxhp0iPz2bkq8Tf61uqyleuQKmw&e=>
Also, there is one hit with this error here:
https://github.com/colvars/colvars/issues/89=X4Iku8BTWbq1vhFT_wKafCW2luDahtDtzy8ZY1rChpk&e=>

Best,
Ajasja

On 23 February 2017 at 01:17, Bennion, Brian <bennion1_at_llnl.gov<mailto:bennion1_at_llnl.gov>> wrote:
Hello,
Getting back to some work I did last year with metadynamics. Hardware has been updated since then as well as the version of namd.
I have scanned the email list for the error described below but have not found anything yet. I know that there has been a fair amount of work in the colvars modules in between namd.10 and namd2.12. Perhaps I just need to alter a keyword. The colvar output is below:

colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2016-10-21.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.81359490&s=AwXHHYXQhAKwCWFMZUJvNVYWlx_0VEG0sGN1IqtMkIU&e=>
colvars: in any publication based on this calculation.
colvars: Using NAMD interface, version 2016-10-20.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "colvarsTrp236ApoAll300nsTripleHillFreq.in":
colvars: # indexFile = "" [default]
colvars: # smp = on [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 500
colvars: # colvarsRestartFrequency = 500
colvars: # colvarsTrajAppend = off [default]
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = on [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "chi1"
colvars: Initializing a new "dihedral" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group1".
colvars: Atom group "group1" defined, 1 atoms initialized: total mass = 14.007, total charge = -0.47.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group2".
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 12.011, total charge = 0.07.
colvars: Initializing atom group "group3".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group3".
colvars: Atom group "group3" defined, 1 atoms initialized: total mass = 12.011, total charge = -0.18.
colvars: Initializing atom group "group4".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Enabling scalable calculation for group "group4".
colvars: Atom group "group4" defined, 1 atoms initialized: total mass = 12.011, total charge = -0.03.
colvars: # oneSiteSystemForce = on
colvars: Error: Feature unavailable: "compute total collective force only from one group center" in uninitialized cvc.
FATAL ERROR: Error in the collective variables module: exiting.

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.

--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU=>
https://github.com/giacomofiorinXD2_iesmWWWM5o4wwzU&e=>
--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin
--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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