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付博， 前天就发现并改正了错误，但是后面还是错了。
colvar.dat 如下：
units gromacs
colvar {
name dist
distance {
group1 { atomNumbers { 2 } }
group2 { atomNumbers { 410} }
}
}
harmonic {
colvars dist
forceConstant 1000
centers 1.52 # initial distance
targetCenters 3.0 # final distance
targetNumSteps 500000
}
错误如下：
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version "2021-03-09".
colvars: Please cite Fiorin et al, Mol Phys 2013:
https://dx.doi.org/10.1080/00268976.2013.813594
in any publication based on this calculation.
colvars: SMP parallelism is enabled; if needed, use "smp off" to override this.
colvars: This version was built with the C++11 standard or higher.
colvars: Using GROMACS interface, version "2021-03-02".
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "colvars.dat":
colvars: # units = "gromacs"
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 100 [default]
colvars: # colvarsRestartFrequency = 0 [default]
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "dist"
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: # centerToOrigin = off [default]
colvars: # centerToReference = off [default]
colvars: # rotateToReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined with 1 atoms requested: total mass = 16, total charge = -0.6318.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerToOrigin = off [default]
colvars: # centerToReference = off [default]
colvars: # rotateToReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined with 1 atoms requested: total mass = 16, total charge = -0.6549.
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: # hardLowerBoundary = on [default]
colvars: # hardUpperBoundary = off [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: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "harmonic1" [default]
colvars: # colvars = { dist }
colvars: # stepZeroData = off [default]
colvars: # outputEnergy = off [default]
colvars: # outputFreq = 0 [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
colvars: # centers = { 1.52 }
colvars: # targetCenters = { 3 }
colvars: # targetNumSteps = 500000
colvars: # targetNumStages = 0 [default]
colvars: # outputAccumulatedWork = off [default]
colvars: # outputCenters = off [default]
colvars: # forceConstant = 1000
colvars: # targetForceConstant = -1 [default]
colvars: The force constant for colvar "dist" will be rescaled to 1000 according to the specified width (1).
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group for variable "dist":0/0. 1 atoms: total mass = 16, total charge = -0.6318.
colvars: Re-initialized atom group for variable "dist":0/1. 1 atoms: total mass = 16, total charge = -0.6549.
colvars: The restart output state file will be "md.restart.colvars.state".
colvars: The final output state file will be "md.colvars.state".
colvars: Opening trajectory file "md.colvars.traj".
Back Off! I just backed up md.colvars.traj to ./#md.colvars.traj.1#
colvars: Error: trying to allocate the collective variable module twice.
colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
-------------------------------------------------------
Program: gmx mdrun, version 2018.8-dev
Source file: src/gromacs/colvars/colvarproxy_gromacs.cpp (line 338)
MPI rank: 0 (out of 6)
Fatal error:
Error in collective variables module.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors |
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楼主 Author
发表于 Post on 2021-4-27 10:17:06