LAMMPS (30 Jul 2016) Reading data file ... orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) 1 by 2 by 3 MPI processor grid reading atoms ... 2004 atoms reading velocities ... 2004 velocities scanning bonds ... 3 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 14 = max dihedrals/atom scanning impropers ... 1 = max impropers/atom reading bonds ... 1365 bonds reading angles ... 786 angles reading dihedrals ... 207 dihedrals reading impropers ... 12 impropers Finding 1-2 1-3 1-4 neighbors ... Special bond factors lj: 0 0 0 Special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 7 = max # of 1-3 neighbors 14 = max # of 1-4 neighbors 18 = max # of special neighbors 84 atoms in group peptide 4 atoms in group one 4 atoms in group two 1 atoms in group ref 9 atoms in group colvar Finding SHAKE clusters ... 19 = # of size 2 clusters 6 = # of size 3 clusters 3 = # of size 4 clusters 640 = # of frozen angles PPPM initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.0228209 estimated relative force accuracy = 6.87243e-05 using double precision FFTs 3d grid and FFT values/proc = 3696 675 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 5 5 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 2 colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2016-08-17. 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 LAMMPS interface, version 2016-04-08. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "peptide.colvars": colvars: # indexFile = "" [default] colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 1000 colvars: # colvarsTrajAppend = off [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = on [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" 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: # forceNoPBC = off [default] colvars: # oneSiteSystemForce = off [default] colvars: Scalable calculation is not available for group "group1" with the current configuration. 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, 4 atoms initialized: total mass = 4, total charge = 0. colvars: Scalable calculation is not available for group "group2" with the current configuration. 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 = 1, total charge = 0. colvars: All components initialized. colvars: # width = 1 [default] colvars: # lowerBoundary = 0 colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 10 colvars: # upperWallConstant = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # timeStepFactor = 1 [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputSystemForce = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "two" 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: # forceNoPBC = off [default] colvars: # oneSiteSystemForce = off [default] colvars: Scalable calculation is not available for group "group1" with the current configuration. 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, 4 atoms initialized: total mass = 4, total charge = 0. colvars: Scalable calculation is not available for group "group2" with the current configuration. 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 = 1, total charge = 0. colvars: All components initialized. colvars: # width = 1 [default] colvars: # lowerBoundary = 0 colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 10 colvars: # upperWallConstant = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # timeStepFactor = 1 [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputSystemForce = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "three" colvars: Initializing a new "gyration" component. colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # scalable = on [default] colvars: Scalable calculation is not available for group "atoms" with the current configuration. colvars: Initializing atom group "atoms". 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 "atoms" defined, 3 atoms initialized: total mass = 3, total charge = 0. colvars: All components initialized. colvars: # width = 1 [default] colvars: # lowerBoundary = 0 colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 10 colvars: # upperWallConstant = 0 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # timeStepFactor = 100 colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputSystemForce = off [default] colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 3 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "metadynamics" instance. colvars: # name = "meta_one" colvars: # colvars = { one, two, three } colvars: # outputEnergy = off [default] colvars: # hillWeight = 10 colvars: # newHillFrequency = 1000 [default] colvars: # hillWidth = 1.25331 [default] colvars: Half-widths of the Gaussian hills (sigma's): colvars: one: 0.626657 colvars: two: 0.626657 colvars: three: 0.626657 colvars: # multipleReplicas = off [default] colvars: # useGrids = on [default] colvars: # gridsUpdateFrequency = 1000 [default] colvars: # rebinGrids = off [default] colvars: # keepHills = off [default] colvars: # writeFreeEnergyFile = on colvars: # saveFreeEnergyFile = off [default] colvars: # writeHillsTrajectory = off [default] colvars: # wellTempered = on colvars: # biasTemperature = 20 colvars: Well-tempered metadynamics is used. colvars: The bias temperature is 20. colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- colvars: The restart output state file will be "rest.colvars.state". colvars: The final output state file will be "out.colvars.state". colvars: Writing to colvar trajectory file "out.colvars.traj". colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011. colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035. colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011. colvars: Re-initialized atom group three:0/0. 3 atoms: total mass = 3.024. [Ross-Mac-Pro2:00469] *** Process received signal *** [Ross-Mac-Pro2:00469] Signal: Segmentation fault: 11 (11) [Ross-Mac-Pro2:00469] Signal code: Address not mapped (1) [Ross-Mac-Pro2:00469] Failing at address: 0x0 [Ross-Mac-Pro2:00469] [ 0] 0 libsystem_platform.dylib 0x00007fff891f5f1a _sigtramp + 26 [Ross-Mac-Pro2:00469] [ 1] 0 ??? 0x0000000000000000 0x0 + 0 [Ross-Mac-Pro2:00469] [ 2] 0 lmp_mpi 0x0000000102c20d72 _ZN6colvar18calc_cvc_gradientsEim + 226 [Ross-Mac-Pro2:00469] [ 3] 0 lmp_mpi 0x0000000102c20807 _ZN6colvar4calcEv + 103 [Ross-Mac-Pro2:00469] [ 4] 0 lmp_mpi 0x0000000102c515a2 _ZN12colvarmodule12calc_colvarsEv + 322 [Ross-Mac-Pro2:00469] [ 5] 0 lmp_mpi 0x0000000102c51129 _ZN12colvarmodule4calcEv + 25 [Ross-Mac-Pro2:00469] [ 6] 0 lmp_mpi 0x00000001027e1083 _ZN18colvarproxy_lammps7computeEv + 227 [Ross-Mac-Pro2:00469] [ 7] 0 lmp_mpi 0x00000001028c35a3 _ZN9LAMMPS_NS10FixColvars10post_forceEi + 1939 [Ross-Mac-Pro2:00469] [ 8] 0 lmp_mpi 0x00000001028c2da7 _ZN9LAMMPS_NS10FixColvars5setupEi + 2087 [Ross-Mac-Pro2:00469] [ 9] 0 lmp_mpi 0x00000001029b91a5 _ZN9LAMMPS_NS6Modify5setupEi + 229 [Ross-Mac-Pro2:00469] [10] 0 lmp_mpi 0x0000000102ba59e7 _ZN9LAMMPS_NS6Verlet5setupEv + 967 [Ross-Mac-Pro2:00469] [11] 0 lmp_mpi 0x0000000102b75f0a _ZN9LAMMPS_NS3Run7commandEiPPc + 3130 [Ross-Mac-Pro2:00469] [12] 0 lmp_mpi 0x0000000102992ba7 _ZN9LAMMPS_NS5Input15command_creatorINS_3RunEEEvPNS_6LAMMPSEiPPc + 55 [Ross-Mac-Pro2:00469] [13] 0 lmp_mpi 0x000000010298ceff _ZN9LAMMPS_NS5Input15execute_commandEv + 1775 [Ross-Mac-Pro2:00469] [14] 0 lmp_mpi 0x000000010298c46e _ZN9LAMMPS_NS5Input4fileEv + 1038 [Ross-Mac-Pro2:00469] [15] 0 lmp_mpi 0x00000001029a12ab main + 75 [Ross-Mac-Pro2:00469] [16] 0 libdyld.dylib 0x00007fff8ca595c9 start + 1 [Ross-Mac-Pro2:00469] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 0 on node Ross-Mac-Pro2 exited on signal 11 (Segmentation fault: 11). --------------------------------------------------------------------------