From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Oct 01 2012 - 15:44:48 CDT
Hello Aron, no, it is not much of an issue in the end, I also ran some
tests for different grid spacings and found no detectable errors, other
than those originating from the finite size of the hills themselves:
whether they are analytically derived or interpolated on a grid it doesn't
matter.
By curiosity, how many hills did you accumulate with hillWidth = 0.05?
On Mon, Oct 1, 2012 at 4:39 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
>
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:08 CST