LAMMPS (27 Jun 2024) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real atom_style full pair_style lj/charmm/coul/long 8.0 10.0 10.0 bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic kspace_style pppm 0.0001 read_data data.peptide Reading data file ... orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462) 1 by 1 by 1 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 orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462) 1 by 1 by 1 MPI processor grid 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 special bonds CPU = 0.000 seconds read_data CPU = 0.012 seconds neighbor 2.0 bin neigh_modify delay 5 timestep 2.0 group peptide type <= 12 84 atoms in group peptide group one id 2 4 5 6 4 atoms in group one group two id 80 82 83 84 4 atoms in group two group ref id 37 1 atoms in group ref group colvar union one two ref 9 atoms in group colvar fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 shell "rm -f peptide2.colvars.*" fix 2 all colvars peptide.colvars2 output peptide2 ---------------------------------------------------------------------- Initializing the collective variables module, version 2024-06-04. Please cite Fiorin et al, Mol Phys 2013: https://doi.org/10.1080/00268976.2013.813594 as well as all other papers listed below for individual features used. Please cite Fiorin et al, Mol Phys 2013: https://doi.org/10.1080/00268976.2013.813594 as well as all other papers listed below for individual features used. Please cite Fiorin et al, Mol Phys 2013: https://doi.org/10.1080/00268976.2013.813594 as well as all other papers listed below for individual features used. This version was built with the C++11 standard or higher. Summary of compile-time features available in this build: - SMP parallelism: enabled (num. threads = 1) - Lepton custom functions: available - Tcl interpreter: not available Using LAMMPS interface, version "2024-07-05". fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 Finding SHAKE clusters ... 19 = # of size 2 clusters 6 = # of size 3 clusters 3 = # of size 4 clusters 640 = # of frozen angles find clusters CPU = 0.000 seconds #dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz #dump_modify 1 sort id thermo_style custom step temp etotal pe ke epair ebond f_2 thermo 10 run 100 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 @Article{Gissinger24, author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor}, title = {Type Label Framework for Bonded Force Fields in LAMMPS}, journal = {J. Phys. Chem. B}, year = 2024, volume = 128, number = 13, pages = {3282–-3297} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.26872465 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.022820853 estimated relative force accuracy = 6.872432e-05 using double precision FFTW3 3d grid and FFT values/proc = 10648 3375 Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule Neighbor list info ... 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 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmm/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard ---------------------------------------------------------------------- Reading new configuration from file "peptide.colvars2": # units = "" [default] # smp = on [default] # colvarsTrajFrequency = 1 # colvarsRestartFrequency = 1000 # scriptedColvarForces = off [default] # scriptingAfterBiases = off [default] ---------------------------------------------------------------------- Initializing a new collective variable. # name = "one" Initializing a new "distance" component. # name = "" [default] # componentCoeff = 1 [default] # componentExp = 1 [default] # period = 0 [default] # wrapAround = 0 [default] # forceNoPBC = off [default] # scalable = on [default] Initializing atom group "group1". # name = "" [default] # centerToOrigin = off [default] # centerToReference = off [default] # rotateToReference = off [default] # atomsOfGroup = "" [default] # indexGroup = "" [default] # psfSegID = [default] # atomsFile = "" [default] # dummyAtom = ( 0 , 0 , 0 ) [default] # enableFitGradients = on [default] # printAtomIDs = off [default] Atom group "group1" defined with 4 atoms requested. Initializing atom group "group2". # name = "" [default] # centerToOrigin = off [default] # centerToReference = off [default] # rotateToReference = off [default] # atomsOfGroup = "" [default] # indexGroup = "" [default] # psfSegID = [default] # atomsFile = "" [default] # dummyAtom = ( 0 , 0 , 0 ) [default] # enableFitGradients = on [default] # printAtomIDs = off [default] Atom group "group2" defined with 4 atoms requested. # oneSiteSystemForce = off [default] # oneSiteTotalForce = off [default] All components initialized. # timeStepFactor = 1 [default] # width = 1 [default] # lowerBoundary = 0 [default] # upperBoundary = 1 [default] # hardLowerBoundary = on [default] # hardUpperBoundary = off [default] # expandBoundaries = off [default] # extendedLagrangian = off [default] # outputValue = on [default] # outputVelocity = off [default] # outputTotalForce = off [default] # outputAppliedForce = off [default] # subtractAppliedForce = off [default] # runAve = off [default] # corrFunc = off [default] ---------------------------------------------------------------------- Collective variables initialized, 1 in total. ---------------------------------------------------------------------- Initializing a new "harmonic" instance. # name = "h_pot" # colvars = { one } # stepZeroData = off [default] # outputEnergy = off [default] # outputFreq = 1000 [default] # timeStepFactor = 1 [default] # writeTISamples = off [default] # writeTIPMF = off [default] # centers = { 10 } # targetCenters = { 10 } [default] # outputCenters = off [default] # forceConstant = 100 # decoupling = off [default] # targetForceConstant = -1 [default] The force constant for colvar "one" will be rescaled to 100 according to the specified width (1). ---------------------------------------------------------------------- Collective variables biases initialized, 1 in total. ---------------------------------------------------------------------- Collective variables module (re)initialized. ---------------------------------------------------------------------- Current simulation parameters: initial step = 0, integration timestep = 2 Updating atomic parameters (masses, charges, etc). Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17. Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16. The final output state file will be "peptide2.colvars.state". Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj". SHAKE stats (type/ave/delta/count) on step 0 Bond: 4 1.111 1.44264e-05 9 Bond: 6 0.996998 7.26967e-06 6 Bond: 8 1.08 1.32536e-05 7 Bond: 10 1.111 1.22749e-05 8 Bond: 12 1.08 1.11767e-05 9 Bond: 14 0.96 0 1 Bond: 18 0.957206 4.37979e-05 1280 Angle: 31 104.519 0.00396029 640 Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes Step Temp TotEng PotEng KinEng E_pair E_bond f_2 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323 10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263 20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314 30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585 40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024 50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863 60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037 70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283 80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186 90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272 SHAKE stats (type/ave/delta/count) on step 100 Bond: 4 1.11096 0.000191462 9 Bond: 6 0.996989 3.55508e-05 6 Bond: 8 1.08 9.0997e-06 7 Bond: 10 1.111 1.58544e-05 8 Bond: 12 1.08 5.80604e-06 9 Bond: 14 0.959997 0 1 Bond: 18 0.957198 2.92445e-05 1280 Angle: 31 104.52 0.00239923 640 100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487 Saving collective variables state to "peptide2.colvars.state". Loop time of 0.907882 on 1 procs for 100 steps with 2004 atoms Performance: 19.033 ns/day, 1.261 hours/ns, 110.146 timesteps/s, 220.734 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71563 | 0.71563 | 0.71563 | 0.0 | 78.82 Bond | 0.0013267 | 0.0013267 | 0.0013267 | 0.0 | 0.15 Kspace | 0.042157 | 0.042157 | 0.042157 | 0.0 | 4.64 Neigh | 0.13452 | 0.13452 | 0.13452 | 0.0 | 14.82 Comm | 0.0034995 | 0.0034995 | 0.0034995 | 0.0 | 0.39 Output | 0.00014584 | 0.00014584 | 0.00014584 | 0.0 | 0.02 Modify | 0.010115 | 0.010115 | 0.010115 | 0.0 | 1.11 Other | | 0.0004888 | | | 0.05 Nlocal: 2004 ave 2004 max 2004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11143 ave 11143 max 11143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 708234 ave 708234 max 708234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 708234 Ave neighs/atom = 353.41018 Ave special neighs/atom = 2.3403194 Neighbor list builds = 13 Dangerous builds = 1 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - Colvars module (Fiorin2013, plus other works listed for specific features) % Colvars module: % Colvars-LAMMPS interface: % Harmonic colvar bias implementation: % Optimal rotation via flexible fitting: % distance colvar component: @article{Fiorin2013, author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome}, title = {Using collective variables to drive molecular dynamics simulations}, journal = {Mol. Phys.}, year = {2013}, volume = {111}, number = {22-23}, pages = {3345--3362}, publisher = {Taylor & Francis}, doi = {10.1080/00268976.2013.813594}, url = {https://doi.org/10.1080/00268976.2013.813594} } % LAMMPS engine: @article{Thompson2022, title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales}, author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.}, journal = {Comp. Phys. Comm.}, volume = {271}, pages = {108171}, year = {2022}, doi = {10.1016/j.cpc.2021.108171}, url = {https://doi.org/10.1016/j.cpc.2021.108171} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Total wall time: 0:00:00