/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib64/nvidia/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64) Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016) Info) http://www.ks.uiuc.edu/Research/vmd/ Info) Email questions and bug reports to vmd@ks.uiuc.edu Info) Please include this reference in published work using VMD: Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38. Info) ------------------------------------------------------------- Info) Multithreading available, 32 CPUs detected. Info) CPU features: SSE2 AVX Info) Free system memory: 60GB (94%) Info) No CUDA accelerator devices available. Info) Dynamically loaded 2 plugins in directory: Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile 2.0 psfplugin) Detected a Charmm PSF file Info) Using plugin psf for structure file ../cdk2_8bS_pocket_wb_ion.psf Info) Analyzing structure ... Info) Atoms: 48310 Info) Bonds: 33898 Info) Angles: 23481 Dihedrals: 13249 Impropers: 798 Cross-terms: 296 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 14774 Info) Waters: 14471 Info) Segments: 12 Info) Fragments: 14477 Protein: 1 Nucleic: 0 0 atomselect0 dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) Info) Using plugin dcd for coordinates from file ../cdk_8bS_pocket_metadyn_75ns_replica1.dcd colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2016-10-26. 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 VMD interface, version 2015-11-02. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "../colvar_grid.txt": colvars: # indexFile = "" [default] colvars: # smp = on [default] colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 100 colvars: # colvarsRestartFrequency = 0 [default] colvars: # colvarsTrajAppend = off [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = on [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "DistLeu83" colvars: Initializing a new "distance" 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: Atom group "group1" defined, 1 atoms initialized: total mass = 14.0067, total charge = -0.8691. 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: Atom group "group2" defined, 1 atoms initialized: total mass = 15.999, total charge = -0.51. colvars: # forceNoPBC = off [default] colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # width = 1 colvars: # lowerBoundary = 0 colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 35 colvars: # upperWallConstant = 800 colvars: # upperWall = 35 colvars: # hardLowerBoundary = on colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = on colvars: # timeStepFactor = 1 [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 = "angle" colvars: Initializing a new "angle" 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: Atom group "group1" defined, 1 atoms initialized: total mass = 15.999, total charge = -0.51. 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: Atom group "group2" defined, 1 atoms initialized: total mass = 14.0067, total charge = -0.8691. 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: Atom group "group3" defined, 1 atoms initialized: total mass = 12.011, total charge = 0.72. colvars: # oneSiteSystemForce = off [default] colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # width = 10 colvars: # lowerBoundary = 0 colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 180 colvars: # upperWallConstant = 0 [default] colvars: # hardLowerBoundary = on colvars: # hardUpperBoundary = on colvars: # expandBoundaries = off colvars: # timeStepFactor = 1 [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: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "metadynamics" instance. colvars: # name = "metadynamics1" [default] colvars: # colvars = { DistLeu83, angle } colvars: # outputEnergy = off [default] colvars: # hillWeight = 0.6 colvars: # newHillFrequency = 1000 colvars: # hillWidth = 1.25 colvars: Half-widths of the Gaussian hills (sigma's): colvars: DistLeu83: 0.625 colvars: angle: 6.25 colvars: # multipleReplicas = off [default] colvars: # useGrids = on [default] colvars: # gridsUpdateFrequency = 1000 [default] colvars: # rebinGrids = on colvars: Metadynamics bias "metadynamics1": Will expand grids when the colvar "DistLeu83" approaches its boundaries. colvars: # keepHills = off [default] colvars: # writeFreeEnergyFile = on colvars: # keepFreeEnergyFiles = off [default] colvars: # writeHillsTrajectory = off [default] colvars: # wellTempered = on colvars: # biasTemperature = 890 colvars: Well-tempered metadynamics is used. colvars: The bias temperature is 890. colvars: # ebMeta = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- colvars: Re-initialized atom group DistLeu83:0/0. 1 atoms: total mass = 14.0067. colvars: Re-initialized atom group DistLeu83:0/1. 1 atoms: total mass = 15.999. colvars: Re-initialized atom group angle:0/0. 1 atoms: total mass = 15.999. colvars: Re-initialized atom group angle:0/1. 1 atoms: total mass = 14.0067. colvars: Re-initialized atom group angle:0/2. 1 atoms: total mass = 12.011. colvars: ---------------------------------------------------------------------- colvars: Restarting from file "../cdk_8bS_pocket_metadyn_75ns_replica1.restart.colvars.state". colvars: Error: total forces are currently not implemented. colvars: If this error message is unclear, try recompiling VMD with -DCOLVARS_DEBUG. colvars: Restarting collective variable "DistLeu83" from value: 20.7703 colvars: Restarting collective variable "angle" from value: 63.0507 colvars: Restarting metadynamics bias "metadynamics1". colvars: Rebinning the energy and forces grids from the grids in the restart file. bigdcd aborting at frame 1 Error: total forces are currently not implemented. Error loading state file bigdcd_done after#0 Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016) Info) Exiting normally. vmd >