From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Oct 01 2012 - 14:21:11 CDT
Hello Jeff, and thanks first of all for researching the causes of the error
plenty!
expandBoundaries is off by default: have you tried running without the
corresponding line altogether?
Most importantly: which version of NAMD are you using? For this particular
feature I strongly recommend 2.9.
Giacomo
On Mon, Oct 1, 2012 at 2:52 PM, Jeff Wereszczynski <
jmweresz_at_mccammon.ucsd.edu> wrote:
> Hello,
>
> I'm trying to run multiple walker metadynamics, however I keep getting the
> following error:
>
> colvars: Error: expandBoundaries is not supported when using more than
> one replicas; please allocate wide enough boundaries for each colvarahead
> of time.
>
> While this sounds straightforward, I've explicitly turned off both
> expandBoundaries and useGrids in my colvars file. Here is the colvars file:
>
>
> -----------------------------------------------------------------------------------
> colvar {
> name rgyr
> expandBoundaries off
> width .1
> lowerboundary 0
> upperboundary 15
> lowerwallconstant 1
> upperwallconstant 1
> gyration {
> atoms {
> atomsFile rgyr.pdb
> atomsCol O
> }
> }
> }
> metadynamics {
> name metad
> colvars rgyr
> hillWeight .2
> hillWidth 10
> newHillFrequency 100
> usegrids false
>
> multipleReplicas on
> replicaID 01
> replicasRegistry replicas
>
> }
>
> -----------------------------------------------------------------------------------
>
> And here is the relevant output in the NAMD log file:
>
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new collective variable.
> colvars: # name = rgyr
> colvars: Initializing a new "gyration" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # period = 0 [default]
> colvars: # wrapAround = 0 [default]
> colvars: Initializing atom group "atoms".
> colvars: Atom group "atoms" defined, 21 initialized: total mass =
> 264.19.
> colvars: All components initialized.
> colvars: # width = 0.1
> colvars: # lowerBoundary = 0
> colvars: # lowerWallConstant = 1
> colvars: # lowerWall = 0 [default]
> colvars: # upperBoundary = 15
> colvars: # upperWallConstant = 1
> colvars: # upperWall = 15 [default]
> *colvars: # expandBoundaries = off
> *colvars: # extendedLagrangian = off [default]
> colvars: # outputValue = on [default]
> colvars: # outputVelocity = off [default]
> colvars: # outputSystemForce = off [default]
> colvars: # outputAppliedForce = off [default]
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables initialized, 1 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new "metadynamics" instance.
> colvars: # name = metad
> colvars: # colvars = { rgyr }
> colvars: # hillWeight = 0.2
> colvars: # newHillFrequency = 100
> colvars: # hillWidth = 10
> colvars: # useGrids = off
> colvars: # multipleReplicas = on
> *colvars: Error: expandBoundaries is not supported when using more than
> one replicas; please allocate wide enough boundaries for each colvarahead
> of time.
> *colvars: If this error message is unclear, try recompiling with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
>
> For clarity, I've bolded the lines that say expandBoundaries is off and
> the error message telling me it isn't. I've tried recompiling NAMD with
> the DCOLVARS_DEBUG flag on, but that didn't provide any more helpful
> information. I also went through the source and found that this error is
> triggered by the expand_grids flag, but I can't figure out where that is
> being set in the code. Any suggestions on this would be greatly
> appreciated!
>
> Also, while I'm asking questions, just for my own sanity have the multiple
> walker + well tempered metadynamics options been tested together? I assume
> there are no major issues I should look out for?
>
> Thanks,
> --
> Jeff Wereszczynski
> Postdoctoral Scholar
> University of California, San Diego
> http://mccammon.ucsd.edu/~jwereszc
>
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