Re: FATAL ERROR: Error in the collective variables module

From: yjcoshc (yjcoshc_at_gmail.com)
Date: Wed May 26 2021 - 05:43:20 CDT

Hi Zhihong,

I suspect you are trying to use ABF or metadynamics to determine the
PMF. Both of the methods require histograms to discretize the CVs, and
in general wall potentials are necessary to keep the CVs inside the
histograms. Historically, the Colvars module implicitly set the wall
boundaries the same as the histogram boundaries (lowerBoundary and
upperBoundary), but recently this behavior has changed, so explicitly
specifying the wall boundaries (lowerWall and upperWall) is mandatory.

In your case, I think you can just add the following lines in your
"restrain01" colvar component:

lowerWall 0

upperWall 8

Best regards,

Haochuan Chen

On 5/26/21 5:19 AM, 辛志宏 wrote:
> Dear namd,
> I came across a issue when I run an example according to the namd
> offical tutorial "Methods for calculating Potentials of Mean Force" by
> namd3 as follows:
>
> I use NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA
>
> How to fix the issue?
> It will be highly appreciate if there are any suggestion.
>
> Zhihong Xin
>
>
> ..........
> colvars:
> ----------------------------------------------------------------------
>
> colvars: Initializing the collective variables module, version
> "2020-02-27".
>
> colvars: Please cite Fiorin et al, Mol Phys 2013:
>
> colvars: https://urldefense.com/v3/__https://dx.doi.org/10.1080/00268976.2013.813594__;!!DZ3fjg!pyVmqjC0qROsYdjEB66MLGSYAJwywH2H7QADwSFLtcGg0CXN2z4nKVEftHbyQCQC9A$
> <https://urldefense.com/v3/__https://dx.doi.org/10.1080/00268976.2013.813594__;!!DZ3fjg!tb9uE3bYl5Bfibz8wQRgWaLBW41ITMHSu2NTGRK-qGDGSSmwZONB2m5FTHhpkLQudw$>
>
> colvars: in any publication based on this calculation.
>
> colvars: SMP parallelism is enabled; if needed, use "smp off" to
> override this.
>
> colvars: This version was built with the C++11 standard or higher.
>
> colvars: Using NAMD interface, version "2019-12-04".
>
> colvars:
> ----------------------------------------------------------------------
>
> colvars: Reading new configuration from file "restrain.in":
>
> colvars: # units = "" [default]
>
> colvars: # smp = on [default]
>
> colvars: # colvarsTrajFrequency = 1000
>
> colvars: # colvarsRestartFrequency = 1000
>
> colvars: # scriptedColvarForces = off [default]
>
> colvars: # scriptingAfterBiases = off [default]
>
> colvars:
> ----------------------------------------------------------------------
>
> colvars:   Initializing a new collective variable.
>
> colvars:   # name = "restrain01"
>
> colvars:   Initializing a new "distanceXY" component.
>
> colvars:     # name = "" [default]
>
> colvars:     # componentCoeff = 1 [default]
>
> colvars:     # componentExp = 1 [default]
>
> colvars:     # period = 0 [default]
>
> colvars:     # wrapAround = 0 [default]
>
> colvars:     # forceNoPBC = off [default]
>
> colvars:     # scalable = on [default]
>
> colvars:       Initializing atom group "main".
>
> colvars:       # name = "" [default]
>
> colvars:       # centerReference = off [default]
>
> colvars:       # rotateReference = off [default]
>
> colvars:       # atomsOfGroup = "" [default]
>
> colvars:       # indexGroup = "" [default]
>
> colvars:       # psfSegID =  [default]
>
> colvars:       # atomsFile = "" [default]
>
> colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
>
> colvars:       # enableForces = on [default]
>
> colvars:       # enableFitGradients = on [default]
>
> colvars:       Enabling scalable calculation for group "main".
>
> colvars:       # printAtomIDs = off [default]
>
> colvars:       Atom group "main" defined with 1 atoms requested: total
> mass = 14.007, total charge = -1.125.
>
> colvars:       Initializing atom group "ref".
>
> colvars:       # name = "" [default]
>
> colvars:       # centerReference = off [default]
>
> colvars:       # rotateReference = off [default]
>
> colvars:       # atomsOfGroup = "" [default]
>
> colvars:       # indexGroup = "" [default]
>
> colvars:       # psfSegID =  [default]
>
> colvars:       # atomsFile = "" [default]
>
> colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
>
> colvars:       # enableForces = on [default]
>
> colvars:       # enableFitGradients = on [default]
>
> colvars:       Enabling scalable calculation for group "ref".
>
> colvars:       # printAtomIDs = off [default]
>
> colvars:       Atom group "ref" defined with 383 atoms requested:
> total mass = 4600.21, total charge = 21.42.
>
> colvars:     # axis = ( 0 , 0 , 1 )
>
> colvars:     # oneSiteSystemForce = off [default]
>
> colvars:     # oneSiteTotalForce = off [default]
>
> colvars:   All components initialized.
>
> colvars:   # timeStepFactor = 1 [default]
>
> colvars:   # width = 0.5
>
> colvars:   # lowerBoundary = 0
>
> colvars:   # upperBoundary = 8
>
> colvars:   Reading legacy options lowerWall and lowerWallConstant:
> consider using a harmonicWalls restraint (caution: force constant
> would then be scaled by width^2).
>
> colvars:   # lowerWall = 0 [default]
>
> FATAL ERROR: Error in the collective variables module (see above for
> details)
>
> colvars: Error: the value of lowerWall must be set explicitly.
>
> FATAL ERROR: Error in the collective variables module (see above for
> details)
>
> [Partition 0][Node 0] End of program
>
>
>

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