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

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Feb 23 2017 - 14:35:22 CST

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

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