From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Feb 23 2017 - 03:10:20 CST
Ajasja pointed correctly to the fix for that bug.
More to that, I believe that the fix is already included in NAMD 2.12: can
you try it?
Giacomo
On Thu, Feb 23, 2017 at 2:36 AM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
wrote:
> Hi!
>
> I'm not 100% sure this is related to your problem, but this was on of the
> larger changes to the colvars module:
> https://colvars.github.io/totalforce.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__colvars.github.io_totalforce.html&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=Nc4rBAmwF0p9LnBBNhMpRiAXvXqyIA8RNz8Kk2kCn90&s=yCbl4Q5dCuBZ-92PFxhp0iPz2bkq8Tf61uqyleuQKmw&e=>
>
> Also, there is one hit with this error here:
> https://github.com/colvars/colvars/issues/89
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_colvars_colvars_issues_89&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=Nc4rBAmwF0p9LnBBNhMpRiAXvXqyIA8RNz8Kk2kCn90&s=X4Iku8BTWbq1vhFT_wKafCW2luDahtDtzy8ZY1rChpk&e=>
>
> Best,
> Ajasja
>
> On 23 February 2017 at 01:17, Bennion, Brian <bennion1_at_llnl.gov> wrote:
>
>> Hello,
>>
>> Getting back to some work I did last year with metadynamics. Hardware
>> has been updated since then as well as the version of namd.
>>
>> I have scanned the email list for the error described below but have not
>> found anything yet. I know that there has been a fair amount of work in
>> the colvars modules in between namd.10 and namd2.12. Perhaps I just need
>> to alter a keyword. The colvar output is below:
>>
>>
>>
>> colvars: ------------------------------------------------------------
>> ----------
>>
>> colvars: Initializing the collective variables module, version 2016-10-21.
>>
>> colvars: Please cite Fiorin et al, Mol Phys 2013:
>>
>> colvars: http://dx.doi.org/10.1080/00268976.2013.813594
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__dx.doi.org_10.1080_00268976.2013.813594&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=Nc4rBAmwF0p9LnBBNhMpRiAXvXqyIA8RNz8Kk2kCn90&s=AwXHHYXQhAKwCWFMZUJvNVYWlx_0VEG0sGN1IqtMkIU&e=>
>>
>> colvars: in any publication based on this calculation.
>>
>> colvars: Using NAMD interface, version 2016-10-20.
>>
>> colvars: ------------------------------------------------------------
>> ----------
>>
>> colvars: Reading new configuration from file
>> "colvarsTrp236ApoAll300nsTripleHillFreq.in":
>>
>> colvars: # indexFile = "" [default]
>>
>> colvars: # smp = on [default]
>>
>> colvars: # analysis = off [default]
>>
>> colvars: # colvarsTrajFrequency = 500
>>
>> colvars: # colvarsRestartFrequency = 500
>>
>> colvars: # colvarsTrajAppend = off [default]
>>
>> colvars: # scriptedColvarForces = off [default]
>>
>> colvars: # scriptingAfterBiases = on [default]
>>
>> colvars: ------------------------------------------------------------
>> ----------
>>
>> colvars: Initializing a new collective variable.
>>
>> colvars: # name = "chi1"
>>
>> colvars: Initializing a new "dihedral" component.
>>
>> colvars: # componentCoeff = 1 [default]
>>
>> colvars: # componentExp = 1 [default]
>>
>> colvars: # period = 0 [default]
>>
>> colvars: # wrapAround = 0 [default]
>>
>> colvars: # scalable = on [default]
>>
>> colvars: Initializing atom group "group1".
>>
>> colvars: # indexGroup = "" [default]
>>
>> colvars: # psfSegID = [default]
>>
>> colvars: # atomsFile = "" [default]
>>
>> colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
>>
>> colvars: # enableForces = on [default]
>>
>> colvars: # centerReference = off [default]
>>
>> colvars: # rotateReference = off [default]
>>
>> colvars: # enableFitGradients = on [default]
>>
>> colvars: Enabling scalable calculation for group "group1".
>>
>> colvars: Atom group "group1" defined, 1 atoms initialized: total
>> mass = 14.007, total charge = -0.47.
>>
>> colvars: Initializing atom group "group2".
>>
>> colvars: # indexGroup = "" [default]
>>
>> colvars: # psfSegID = [default]
>>
>> colvars: # atomsFile = "" [default]
>>
>> colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
>>
>> colvars: # enableForces = on [default]
>>
>> colvars: # centerReference = off [default]
>>
>> colvars: # rotateReference = off [default]
>>
>> colvars: # enableFitGradients = on [default]
>>
>> colvars: Enabling scalable calculation for group "group2".
>>
>> colvars: Atom group "group2" defined, 1 atoms initialized: total
>> mass = 12.011, total charge = 0.07.
>>
>> colvars: Initializing atom group "group3".
>>
>> colvars: # indexGroup = "" [default]
>>
>> colvars: # psfSegID = [default]
>>
>> colvars: # atomsFile = "" [default]
>>
>> colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
>>
>> colvars: # enableForces = on [default]
>>
>> colvars: # centerReference = off [default]
>>
>> colvars: # rotateReference = off [default]
>>
>> colvars: # enableFitGradients = on [default]
>>
>> colvars: Enabling scalable calculation for group "group3".
>>
>> colvars: Atom group "group3" defined, 1 atoms initialized: total
>> mass = 12.011, total charge = -0.18.
>>
>> colvars: Initializing atom group "group4".
>>
>> colvars: # indexGroup = "" [default]
>>
>> colvars: # psfSegID = [default]
>>
>> colvars: # atomsFile = "" [default]
>>
>> colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
>>
>> colvars: # enableForces = on [default]
>>
>> colvars: # centerReference = off [default]
>>
>> colvars: # rotateReference = off [default]
>>
>> colvars: # enableFitGradients = on [default]
>>
>> colvars: Enabling scalable calculation for group "group4".
>>
>> colvars: Atom group "group4" defined, 1 atoms initialized: total
>> mass = 12.011, total charge = -0.03.
>>
>> colvars: # oneSiteSystemForce = on
>>
>> colvars: Error: Feature unavailable: "compute total collective force only
>> from one group center" in uninitialized cvc.
>>
>> FATAL ERROR: Error in the collective variables module: exiting.
>>
>>
>>
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>>
>> Reason: FATAL ERROR: Error in the collective variables module: exiting.
>>
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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