Re: expandBoundaries and multiple walker metadynamics

From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Oct 01 2012 - 15:13:41 CDT

That is strange, I have multiple replicas MetaDynamics working in 2.9.
I've never tried without useGrids, however. I assume the useGrids is off
because of the smaller increment size of the colvar?

~Aron

On Mon, Oct 1, 2012 at 3:52 PM, Jeff Wereszczynski <
jmweresz_at_mccammon.ucsd.edu> wrote:

> Hi Giacomo,
>
> I have tried leaving out that flag all together, in fact thats how I
> originally had it set up, and I still get that error.
>
> Also, I am using version 2.9. I considered trying the CVS, but a
> quick look at the online change logs made it seem as if nothing in the
> colvars routines had been touched since the 2.9 release. I could
> always give that a try though...
>
> Thanks,
> Jeff
>
> On Mon, Oct 1, 2012 at 12:21 PM, Giacomo Fiorin
> <giacomo.fiorin_at_gmail.com> wrote:
> > 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
> >
> >
>
>
>
> --
> Jeff Wereszczynski
> Postdoctoral Scholar
> University of California, San Diego
> http://mccammon.ucsd.edu/~jwereszc
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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