From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Oct 01 2012 - 16:15:36 CDT
Indeed: if you only changed "width" you always changed the spacing of the
grid and the width of the hill in the same proportion, i.e. you were
working on the "safe side" all along. What you did was actually adding
more resolution to detect ruggedness in the PMF that wasn't really there,
given the simplicity of the water dimer.
On Mon, Oct 1, 2012 at 4:54 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> That's true, I forgot about that little factor of the hillwidth. I guess
> I've always left that as the default, which means when I tested 0.05 width,
> the hillwidth was actually ~0.06? So the conclusion about it not being a
> big deal should still stand.
>
> ~Aron
>
>
> On Mon, Oct 1, 2012 at 4:50 PM, Jeff Wereszczynski <
> jmweresz_at_mccammon.ucsd.edu> wrote:
>
>> Hi Aron,
>>
>> My understanding was that the 1.0 applies to the hillWidth parameter
>> in the metadynamics section, and not the width parameter in the colvar
>> section, which is why I set it up with width=0.1 and hillWidth=10. Of
>> course, I'll look into this more and do some testing before beginning
>> production runs.
>>
>> Thanks again for your help!
>> Jeff
>>
>> On Mon, Oct 1, 2012 at 1:39 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>> > Glad to hear it worked. The grids certainly help over the course of a
>> long
>> > simulation with many hills also. The one concern here is that the
>> manual
>> > mentions that with useGrids on the colvar width should ideally not be
>> less
>> > then 1.0 to avoid problems discretizing the potential onto the grids.
>> Since
>> > your width is 0.1 that might be an issue. That being said, I've done
>> some
>> > simple test cases with a water dimer and a distance colvar with a width
>> of
>> > 0.05 and the results are identical in the long to a larger width (though
>> > obviously smoother) so perhaps it isn't an issue afterall?
>> >
>> > ~Aron
>> >
>> >
>> > 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
>> >
>> >
>> >
>> >
>> > --
>> > 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
>>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
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