From: Jeff Wereszczynski (jmweresz_at_mccammon.ucsd.edu)
Date: Mon Oct 01 2012 - 15:24:46 CDT
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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