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output of a weird simulation
Info: NAMD Git-2018-07-23 for Linux-x86_64-multicore
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60800 for multicore-linux64
Info: Built Mon Jul 23 12:36:38 CEST 2018 by bcz on atenea
Info: 1 NAMD Git-2018-07-23 Linux-x86_64-multicore 32 atenea bcz
Info: Running on 32 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0351501 s
CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue
Info: 2077.75 MB of memory in use based on /proc/self/stat
Info: Configuration file is continue_metadynamics_04.namd
...
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-07-20.
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: SMP parallelism is available.
colvars: Using NAMD interface, version 2018-07-20.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "cont_meta_04.namd":
colvars: # indexFile = "" [default]
colvars: # smp = on [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 500
colvars: # colvarsRestartFrequency = 3000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "DistanceZ"
colvars: Initializing a new "distanceZ" 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 "main".
colvars: # name = "" [default]
colvars: # centerReference = on
colvars: # rotateReference = on
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "../input/reference.pdb"
colvars: # atomsCol = "O"
colvars: # atomsColValue = 2
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: Within atom group "main":
colvars: Initializing atom group "fittingGroup".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "../input/reference.pdb"
colvars: # atomsCol = "O"
colvars: # atomsColValue = 1
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "fittingGroup" defined, 31 atoms initialized: total mass = 372.341, total charge = 1.89.
colvars: # refPositions = [default]
colvars: # refPositionsFile = "../input/reference.pdb"
colvars: # refPositionsCol = "" [default]
colvars: Warning: atom group "main" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates.
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "main" defined, 18 atoms initialized: total mass = 216.198, total charge = -2.273.
colvars: Initializing atom group "ref".
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 = ( -0.009 , 0.95 , 0.936 )
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "ref" defined, 0 atoms initialized: total mass = 1, total charge = 0.
colvars: # axis = ( 0.332 , 0.898 , -0.288 )
colvars: The normalized axis is: ( 0.332071 , 0.898192 , -0.288062 ).
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 0.1
colvars: # lowerBoundary = -10
colvars: # upperBoundary = 10
colvars: # hardLowerBoundary = off [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: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "DistanceXY"
colvars: Initializing a new "distanceXY" 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 "main".
colvars: # name = "" [default]
colvars: # centerReference = on
colvars: # rotateReference = on
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "../input/reference.pdb"
colvars: # atomsCol = "O"
colvars: # atomsColValue = 2
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: Within atom group "main":
colvars: Initializing atom group "fittingGroup".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "../input/reference.pdb"
colvars: # atomsCol = "O"
colvars: # atomsColValue = 1
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "fittingGroup" defined, 31 atoms initialized: total mass = 372.341, total charge = 1.89.
colvars: # refPositions = [default]
colvars: # refPositionsFile = "../input/reference.pdb"
colvars: # refPositionsCol = "" [default]
colvars: Warning: atom group "main" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates.
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "main" defined, 18 atoms initialized: total mass = 216.198, total charge = -2.273.
colvars: Initializing atom group "ref".
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 = ( -0.09 , 0.95 , 0.936 )
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "ref" defined, 0 atoms initialized: total mass = 1, total charge = 0.
colvars: # axis = ( 0.332 , 0.898 , -0.288 )
colvars: The normalized axis is: ( 0.332071 , 0.898192 , -0.288062 ).
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 0.1
colvars: # lowerBoundary = 0
colvars: # upperBoundary = 5
colvars: # hardLowerBoundary = off [default]
colvars: # hardUpperBoundary = off [default]
colvars: # expandBoundaries = on
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: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonicwalls" instance.
colvars: # name = "ha"
colvars: # colvars = { DistanceXY }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
colvars: # forceConstant = 1 [default]
colvars: # targetForceConstant = -1 [default]
colvars: # lowerWalls = { 0 }
colvars: # upperWalls = { 5 }
colvars: # lowerWallConstant = 5
colvars: # upperWallConstant = 5
colvars: The lower wall force constant for colvar "DistanceXY" will be rescaled to 500 according to the specified width.
colvars: The upper wall force constant for colvar "DistanceXY" will be rescaled to 500 according to the specified width.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "metadynamics" instance.
colvars: # name = "meta_04_wtmetad"
colvars: # colvars = { DistanceZ }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
colvars: # hillWeight = 0.1
colvars: # newHillFrequency = 500
colvars: # hillWidth = 0.16
colvars: Half-widths of the Gaussian hills (sigma's):
colvars: DistanceZ: 0.008
colvars: # multipleReplicas = off [default]
colvars: # useGrids = on [default]
colvars: # gridsUpdateFrequency = 500 [default]
colvars: # rebinGrids = off [default]
colvars: # keepHills = off [default]
colvars: # writeFreeEnergyFile = on [default]
colvars: # keepFreeEnergyFiles = off [default]
colvars: # writeHillsTrajectory = on
colvars: # wellTempered = on
colvars: # biasTemperature = 4500
colvars: Well-tempered metadynamics is used.
colvars: The bias temperature is 4500.
colvars: # ebMeta = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Updating NAMD interface:
colvars: Warning: enabling wrapAll can lead to inconsistent results for Colvars calculations: please disable wrapAll, as is the default option in NAMD.
colvars: updating atomic data (49 atoms).
colvars: updating group data (0 scalable groups, 0 atoms in total).
colvars: Re-initialized atom group DistanceZ:0/0. 18 atoms: total mass = 216.198.
colvars: Re-initialized atom group DistanceZ:0/1. 0 atoms: total mass = 1.
colvars: Re-initialized atom group DistanceXY:0/0. 18 atoms: total mass = 216.198.
colvars: Re-initialized atom group DistanceXY:0/1. 0 atoms: total mass = 1.
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "ligA_bb_md.colvars.state".
colvars: This state file was generated with version 2018-09-07
colvars: Restarting collective variable "DistanceZ" from value: -10.3168
colvars: Restarting collective variable "DistanceXY" from value: 4.0201
colvars: Read 20365 hills in addition to the grids.
colvars: 20365 hills are near the grid boundaries: they will be computed analytically and saved to the state files.
colvars: ----------------------------------------------------------------------
colvars: The restart output state file will be "ligA_bb_md_cont1.restart.colvars.state".
colvars: The final output state file will be "ligA_bb_md_cont1.colvars.state".
colvars: Writing to colvar trajectory file "ligA_bb_md_cont1.colvars.traj".
colvars: Initializing step number as firstTimestep.
Info: useSync: 0 useProxySync: 0
Info: Startup phase 13 took 1.78042 s, 2125.87 MB of memory in use
Info: Startup phase 14 took 0.000202894 s, 2125.87 MB of memory in use
Info: Startup phase 15 took 0.000917196 s, 2126.38 MB of memory in use
Info: Finished startup at 3.05126 s, 2126.38 MB of memory in use
TCL: Running for 50000000 steps
colvars: Updating NAMD interface:
colvars: Warning: enabling wrapAll can lead to inconsistent results for Colvars calculations: please disable wrapAll, as is the default option in NAMD.
colvars: updating atomic data (49 atoms).
colvars: updating group data (0 scalable groups, 0 atoms in total).
colvars: Re-initialized atom group DistanceZ:0/0. 18 atoms: total mass = 216.198.
colvars: Re-initialized atom group DistanceZ:0/1. 0 atoms: total mass = 1.
colvars: Re-initialized atom group DistanceXY:0/0. 18 atoms: total mass = 216.198.
colvars: Re-initialized atom group DistanceXY:0/1. 0 atoms: total mass = 1.
colvars: The restart output state file will be "ligA_bb_md_cont1.restart.colvars.state".
colvars: The final output state file will be "ligA_bb_md_cont1.colvars.state".
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