From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Oct 01 2012 - 15:40:18 CDT
Hi Jeff, you're right, it shouldn't crash: I'm currently trying to find out
the reason of the error.
And yes, my message that you linked refers to an older version:
the metadynamics code in NAMD 2.9 is fully grids-enabled. Please disregard
it, and refer instead to the latest version of the user's guide.
At the present stage you should only set useGrids = off for testing /
debugging, or to apply metadynamics to distanceDir- or orientation-based
variables, that do not have a simple mapping on a Cartesian grid. For
anything else, I recommend leaving useGrids to on as per the default.
Giacomo
On Mon, Oct 1, 2012 at 4:24 PM, Jeff Wereszczynski <
jmweresz_at_mccammon.ucsd.edu> wrote:
> Well that IS funny! I had turned off the usegrids option because I
> had assumed it wouldn't work based on this previous mailing list
> entry:
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/11810.html
>
> However, if I put it back on then it works fine. Apparently the use
> of grids in multiple replica metadynamics has been enabled? Still, it
> probably shouldn't crash if you don't use grids.
>
> Thanks!
> Jeff
>
> On Mon, Oct 1, 2012 at 1:13 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> > 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
> >
>
>
>
> --
> Jeff Wereszczynski
> Postdoctoral Scholar
> University of California, San Diego
> http://mccammon.ucsd.edu/~jwereszc
>
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