From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Wed Feb 22 2017 - 18:17:44 CST
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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