From: Jeff Wereszczynski (jmweresz_at_mccammon.ucsd.edu)
Date: Mon Oct 01 2012 - 14:52:08 CDT
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
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