Re: expandBoundaries and multiple walker metadynamics

From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Oct 01 2012 - 15:54:32 CDT

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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:08 CST