Re: Multi canonical ensemble method

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Sep 30 2019 - 06:49:46 CDT

Dear Takeru,

this "failed dependency" message indicates that ABF only supports scalar
variables. A multidimensional ABF calculation can be done with several
scalar variables, not a single vector one.

In this case, the orientation variable is 4-dimensional, which is probably
too much for ABF anyway. I recommend reducing your sampling space to 1, 2
or 3 scalar quantities.

Best wishes,
Jerome

On Mon, 30 Sep 2019 at 04:23, Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp>
wrote:

> Dear all.
>
> Hi. I am trying multi-canonical ensemble method using NAMD2.13.
>
> I wrote colvar file as follows:
>
> colvarsTrajFrequency 5000
> colvarsRestartFrequency 50000
>
> colvar {
> name theta
>
> outputValue on
> #outputVelocity on
> #outputEnergy on
> #outputSystemForce on
> #outputAppliedForce on
>
> orientation {
> atoms { atomnumbers {
> 13754 13755 13756 13757 13758 13761 13783 13785 19290
> 19291 19292 19293 19294 19297 19319 19321
> }}
> refPositionsFile ./colvar.pdb
> refPositionsCol O
> }
> }
>
> abf {
> colvars theta
> fullSamples 200
> hideJacobian
> }
>
>
> Then, we execute simulation, following error was output:
>
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 2018-10-16.
> 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: SMP parallelism is available.
> colvars: Using NAMD interface, version 2018-08-29.
> colvars:
> ----------------------------------------------------------------------
> colvars: Reading new configuration from file "colvar.in":
> colvars: # smp = on [default]
> colvars: # analysis = off [default]
> colvars: # colvarsTrajFrequency = 5000
> colvars: # colvarsRestartFrequency = 50000
> colvars: # scriptedColvarForces = off [default]
> colvars: # scriptingAfterBiases = off [default]
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new collective variable.
> colvars: # name = "theta"
> colvars: Initializing a new "orientation" 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 "atoms".
> 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: # printAtomIDs = off [default]
> colvars: Atom group "atoms" defined, 16 atoms initialized: total
> mass = 195.991, total charge = -1.86.
> colvars: # refPositions = [default]
> colvars: # refPositionsFile = "./colvar.pdb"
> colvars: # refPositionsCol = "O"
> colvars: # refPositionsColValue = 0 [default]
> Info: Found 351 unique exclusion lists needing 1152 bytes
> Info: Found 351 unique exclusion lists needing 1152 bytes
> Info: Found 351 unique exclusion lists needing 1152 bytes
> Info: Found 351 unique exclusion lists needing 1152 bytes
> colvars: Centering the reference coordinates: it is assumed that each
> atom is the closest periodic image to the center of geometry.
> colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default]
> colvars: All components initialized.
> colvars: # timeStepFactor = 1 [default]
> colvars: # width = 1 [default]
> colvars: # expandBoundaries = off [default]
> colvars: # extendedLagrangian = off [default]
> colvars: # outputValue = on
> colvars: # outputVelocity = off [default]
> colvars: # outputTotalForce = off [default]
> colvars: # outputAppliedForce = off [default]
> colvars: # subtractAppliedForce = off [default]
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables initialized, 1 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new "abf" instance.
> colvars: # name = "abf1" [default]
> colvars: # colvars = { theta }
> colvars: # outputEnergy = off [default]
> colvars: # timeStepFactor = 1 [default]
> colvars: Static feature "scalar" may not be enabled as a dependency in
> colvar theta.
> colvars: ...required by "require scalar variables" in bias abf1
> colvars: Error: Failed dependency in bias abf1.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> Any parts of configulation file was wrong?
>
>
>
> Best wishes,
> Takeru Kameda
> PhD Student, Hiroshima University, Japan
>
>

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