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November 13, 2018 16:14
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output of a weird simulation
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| 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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