Colvars dashboard - colvars do not appear

[balazsfabian]

I tried to create a distance colvar using the dashboard (version 2023.01.11).

• I load my trajectory
• Open the dashboard
• Click "New" and accept the proposed distance colvar

The colvar does not appear in the main window. When I click where it should be, I receive: Error: can't read "cfg": no such variable which is the same message I get when I do not create a colvar at all.

Finally, if I try to create a colvar with the same name, the dashboard complains that it already exists.

[jhenin]

Thanks for the report @balazsfabian ! I think this may be fixed already. Can you please try the current master branch? Just copy the cv_dashboard directory over the VMD plugin installation, or use the provided Makefile. See README for details: https://github.com/Colvars/colvars/tree/master/vmd/cv_dashboard

We are eagerly waiting for a new VMD release with various updates.

[balazsfabian]

Thank you for the quick reply, @jhenin ! I now tried version 2024.02.17, and the issue persists. Are there any other checks that I could do?

The detailed versions are:

Colvars Dashboard, version 2024.02.17
Graphical user interface for the Colvars Module, version 2019-05-22
https://colvars.github.io

In VMD for LINUXAMD64, version 1.9.4a38 (October 17,2019)
Running Tcl/TK 8.5.6

I also have the following text in the tcl-console:

colvars: ----------------------------------------------------------------------
colvars: Reading new configuration:
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 0 [default]
colvars: # colvarsRestartFrequency = 0 [default]
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new collective variable.
colvars:   # name = "myColvar"
colvars:   Initializing a new "distance" component.
colvars:     # name = "" [default]
colvars:     # componentCoeff = 1 [default]
colvars:     # componentExp = 1 [default]
colvars:     # period = 0 [default]
colvars:     # wrapAround = 0 [default]
colvars:     # forceNoPBC = off [default]
colvars:     # scalable = on [default]
colvars:       Initializing atom group "group1".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group1" defined with 2 atoms requested: total mass = 15.0146, total charge = 0.
colvars:       Initializing atom group "group2".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group2" defined with 2 atoms requested: total mass = 13.0186, total charge = 0.
colvars:     # oneSiteSystemForce = off [default]
colvars:     # oneSiteTotalForce = off [default]
colvars:   All components initialized.
colvars:   # timeStepFactor = 1 [default]
colvars:   # width = 1 [default]
colvars:   # lowerBoundary = 0 [default]
colvars:   # upperBoundary = 0 [default]
colvars:   # expandBoundaries = off [default]
colvars:   # extendedLagrangian = off [default]
colvars:   # outputValue = on [default]
colvars:   # outputVelocity = off [default]
colvars:   # outputTotalForce = off [default]
colvars:   # outputAppliedForce = off [default]
colvars:   # subtractAppliedForce = off [default]
colvars:   # runAve = off [default]
colvars:   # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: No collective variables biases were defined.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group for variable "myColvar":0/0. 2 atoms: total mass = 15.0146, total charge = 0.
colvars: Re-initialized atom group for variable "myColvar":0/1. 2 atoms: total mass = 13.0186, total charge = 0.

[jhenin]

Strange! VMD 1.9.4a38 is an older alpha version though, with an old Colvars interface. Can you try 1.9.4a55?

[balazsfabian]

Thank for the recommendation, @jhenin ! We updated right to 1.9.4a57, and it works!