From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Feb 23 2017 - 01:36:03 CST
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
Also, there is one hit with this error here:
https://github.com/colvars/colvars/issues/89
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
>
> 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.
>
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