diff --git a/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.1 deleted file mode 100644 index 1003b9729e..0000000000 --- a/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.1 +++ /dev/null @@ -1,629 +0,0 @@ -LAMMPS (27 Nov 2018) - 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 - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 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 - reading bonds ... - 1365 bonds - reading angles ... - 786 angles - reading dihedrals ... - 207 dihedrals - reading impropers ... - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -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 out*.colvars.*" -fix 2 all colvars peptide.colvars -fix 2a ref setforce 0.0 0.0 0.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.colvar.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 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 10648 3375 -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/newton - bin: standard -colvars: Creating proxy instance -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. -colvars: Using LAMMPS interface, version 2018-08-29. -colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "peptide.colvars": -colvars: # smp = on [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "one" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "two" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = "h_pot" -colvars: # colvars = { one, two } -colvars: # outputEnergy = off [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 100 -colvars: # targetForceConstant = -1 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module (re)initialized. -colvars: ---------------------------------------------------------------------- -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1. -colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1. -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: Performing analysis. -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 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 292.14604 - 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 - 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 - 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 - 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 - 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 - 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 - 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 - 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 - 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97155e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84253e-05 - 12 1.08 7.2713e-06 - 14 0.959996 0 - 18 0.957198 3.36079e-05 - 31 104.52 0.0030599 - 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 -colvars: Saving collective variables state to "out.colvars.state". -Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms - -Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s -98.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.5817 | 1.5817 | 1.5817 | 0.0 | 72.79 -Bond | 0.0031469 | 0.0031469 | 0.0031469 | 0.0 | 0.14 -Kspace | 0.17366 | 0.17366 | 0.17366 | 0.0 | 7.99 -Neigh | 0.37354 | 0.37354 | 0.37354 | 0.0 | 17.19 -Comm | 0.013652 | 0.013652 | 0.013652 | 0.0 | 0.63 -Output | 0.00026059 | 0.00026059 | 0.00026059 | 0.0 | 0.01 -Modify | 0.025484 | 0.025484 | 0.025484 | 0.0 | 1.17 -Other | | 0.001615 | | | 0.07 - -Nlocal: 2004 ave 2004 max 2004 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11124 ave 11124 max 11124 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 708237 ave 708237 max 708237 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 708237 -Ave neighs/atom = 353.412 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 12 -Dangerous builds = 2 - -run 100 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 10648 3375 -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. -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97155e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84253e-05 - 12 1.08 7.2713e-06 - 14 0.959996 0 - 18 0.957198 3.36079e-05 - 31 104.52 0.0030599 -Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond f_2 - 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 - 110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657 - 120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812 - 130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592 - 140 253.85111 -5452.1838 -6473.4522 1021.2684 -6609.4826 26.071651 0.30585517 - 150 261.31816 -5490.4727 -6541.7817 1051.3091 -6646.6076 16.258823 6.9051008 - 160 255.7352 -5521.5941 -6550.4424 1028.8483 -6658.1373 19.717399 12.339679 - 170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217 - 180 248.51161 -5550.3253 -6550.1124 999.78705 -6661.4235 26.200127 3.4336038 - 190 250.80862 -5555.2554 -6564.2836 1009.0282 -6666.164 25.53634 3.3494288 -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.81266e-06 - 6 0.997 7.79424e-07 - 8 1.08 1.08903e-06 - 10 1.111 2.96503e-07 - 12 1.08 4.69038e-07 - 14 0.960001 0 - 18 0.957201 3.76471e-06 - 31 104.52 0.000411055 - 200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574 -colvars: Saving collective variables state to "out.colvars.state". -Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms - -Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s -98.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.5975 | 1.5975 | 1.5975 | 0.0 | 78.58 -Bond | 0.0033164 | 0.0033164 | 0.0033164 | 0.0 | 0.16 -Kspace | 0.17349 | 0.17349 | 0.17349 | 0.0 | 8.53 -Neigh | 0.21971 | 0.21971 | 0.21971 | 0.0 | 10.81 -Comm | 0.012045 | 0.012045 | 0.012045 | 0.0 | 0.59 -Output | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.01 -Modify | 0.025034 | 0.025034 | 0.025034 | 0.0 | 1.23 -Other | | 0.001596 | | | 0.08 - -Nlocal: 2004 ave 2004 max 2004 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11159 ave 11159 max 11159 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 708083 ave 708083 max 708083 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 708083 -Ave neighs/atom = 353.335 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 7 -Dangerous builds = 0 - -fix 2 all colvars peptide.colvars input out.colvars.state output out2 -colvars: Resetting the Collective Variables module. - -run 100 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 10648 3375 -colvars: Creating proxy instance -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. -colvars: Using LAMMPS interface, version 2018-08-29. -colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "peptide.colvars": -colvars: # smp = on [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "one" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "two" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = "h_pot" -colvars: # colvars = { one, two } -colvars: # outputEnergy = off [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 100 -colvars: # targetForceConstant = -1 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module (re)initialized. -colvars: ---------------------------------------------------------------------- -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1. -colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1. -colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "out.colvars.state". -colvars: Restarting collective variable "one" from value: 10.0128 -colvars: Restarting collective variable "two" from value: 9.62236 -colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out2.colvars.state". -colvars: Writing to colvar trajectory file "out2.colvars.traj". -colvars: Setting initial step number from LAMMPS: 200 -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: Performing analysis. -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.81266e-06 - 6 0.997 7.79424e-07 - 8 1.08 1.08903e-06 - 10 1.111 2.96503e-07 - 12 1.08 4.69038e-07 - 14 0.960001 0 - 18 0.957201 3.76471e-06 - 31 104.52 0.000411055 -Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond f_2 - 200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574 - 210 253.15303 -5538.5615 -6557.0215 1018.46 -6672.0498 37.67662 0.61219496 - 220 245.19621 -5522.519 -6508.9679 986.44888 -6628.1899 36.657688 0.04864338 - 230 258.69884 -5495.7275 -6536.4988 1040.7713 -6658.2885 34.857911 0.22092547 - 240 260.79635 -5469.8678 -6519.0776 1049.2098 -6624.1801 31.576951 3.7574816 - 250 269.07527 -5438.3946 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600014 - 260 266.01049 -5397.3485 -6467.5353 1070.1868 -6580.2897 26.871917 8.3323097 - 270 272.81313 -5350.882 -6448.4365 1097.5545 -6563.8231 23.114195 10.973131 - 280 279.42263 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644027 8.5490492 - 290 286.85172 -5260.841 -6414.8741 1154.0331 -6515.6798 28.574838 5.9100133 -SHAKE stats (type/ave/delta) on step 300 - 4 1.111 1.79792e-05 - 6 0.997005 1.02512e-05 - 8 1.08 1.85102e-05 - 10 1.111 9.98839e-06 - 12 1.08 8.84111e-06 - 14 0.960008 0 - 18 0.957203 1.8445e-05 - 31 104.52 0.00168383 - 300 291.52798 -5216.288 -6389.1341 1172.8462 -6503.1276 27.889154 2.2482459 -colvars: Saving collective variables state to "out2.colvars.state". -Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms - -Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s -98.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.6047 | 1.6047 | 1.6047 | 0.0 | 77.46 -Bond | 0.0031033 | 0.0031033 | 0.0031033 | 0.0 | 0.15 -Kspace | 0.17325 | 0.17325 | 0.17325 | 0.0 | 8.36 -Neigh | 0.25117 | 0.25117 | 0.25117 | 0.0 | 12.12 -Comm | 0.012173 | 0.012173 | 0.012173 | 0.0 | 0.59 -Output | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01 -Modify | 0.025317 | 0.025317 | 0.025317 | 0.0 | 1.22 -Other | | 0.001731 | | | 0.08 - -Nlocal: 2004 ave 2004 max 2004 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11296 ave 11296 max 11296 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 708152 ave 708152 max 708152 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 708152 -Ave neighs/atom = 353.369 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 8 -Dangerous builds = 0 - -colvars: Resetting the Collective Variables module. - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:06 diff --git a/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.4 deleted file mode 100644 index 91ef59b619..0000000000 --- a/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.4 +++ /dev/null @@ -1,629 +0,0 @@ -LAMMPS (27 Nov 2018) - 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 - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 2 by 2 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 - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -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 out*.colvars.*" -fix 2 all colvars peptide.colvars -fix 2a ref setforce 0.0 0.0 0.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.colvar.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 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 4312 960 -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/newton - bin: standard -colvars: Creating proxy instance -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. -colvars: Using LAMMPS interface, version 2018-08-29. -colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "peptide.colvars": -colvars: # smp = on [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "one" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "two" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = "h_pot" -colvars: # colvars = { one, two } -colvars: # outputEnergy = off [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 100 -colvars: # targetForceConstant = -1 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module (re)initialized. -colvars: ---------------------------------------------------------------------- -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1. -colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1. -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: Performing analysis. -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 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 292.14604 - 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 - 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 - 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 - 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 - 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 - 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 - 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 - 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 - 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97155e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84253e-05 - 12 1.08 7.2713e-06 - 14 0.959996 0 - 18 0.957198 3.36079e-05 - 31 104.52 0.0030599 - 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 -colvars: Saving collective variables state to "out.colvars.state". -Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms - -Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.40413 | 0.41468 | 0.42573 | 1.4 | 67.52 -Bond | 0.00056815 | 0.0011595 | 0.0017791 | 1.6 | 0.19 -Kspace | 0.056367 | 0.066512 | 0.076213 | 3.3 | 10.83 -Neigh | 0.095025 | 0.09507 | 0.095124 | 0.0 | 15.48 -Comm | 0.015385 | 0.015831 | 0.01623 | 0.2 | 2.58 -Output | 0.00026512 | 0.00034493 | 0.00057554 | 0.0 | 0.06 -Modify | 0.01938 | 0.019431 | 0.019474 | 0.0 | 3.16 -Other | | 0.001141 | | | 0.19 - -Nlocal: 501 ave 513 max 489 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Nghost: 6563.25 ave 6596 max 6519 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 177059 ave 181742 max 172942 min -Histogram: 1 0 1 0 0 0 1 0 0 1 - -Total # of neighbors = 708237 -Ave neighs/atom = 353.412 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 12 -Dangerous builds = 2 - -run 100 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 4312 960 -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. -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97155e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84253e-05 - 12 1.08 7.2713e-06 - 14 0.959996 0 - 18 0.957198 3.36079e-05 - 31 104.52 0.0030599 -Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond f_2 - 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 - 110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657 - 120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812 - 130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592 - 140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517 - 150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008 - 160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679 - 170 253.42527 -5540.0941 -6559.6493 1019.5552 -6656.6677 23.293812 10.290217 - 180 248.51161 -5550.3253 -6550.1124 999.78704 -6661.4235 26.200127 3.4336037 - 190 250.80862 -5555.2553 -6564.2834 1009.0282 -6666.1638 25.53634 3.3494287 -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.81266e-06 - 6 0.997 7.79424e-07 - 8 1.08 1.08903e-06 - 10 1.111 2.96503e-07 - 12 1.08 4.69038e-07 - 14 0.960001 0 - 18 0.957201 3.76471e-06 - 31 104.52 0.000411055 - 200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572 -colvars: Saving collective variables state to "out.colvars.state". -Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms - -Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.40512 | 0.41306 | 0.42363 | 1.3 | 72.50 -Bond | 0.00061107 | 0.001151 | 0.0017512 | 1.4 | 0.20 -Kspace | 0.054393 | 0.063988 | 0.07198 | 3.0 | 11.23 -Neigh | 0.056063 | 0.056079 | 0.05609 | 0.0 | 9.84 -Comm | 0.013584 | 0.014145 | 0.014649 | 0.3 | 2.48 -Output | 0.00026965 | 0.00042897 | 0.00090265 | 0.0 | 0.08 -Modify | 0.019253 | 0.019257 | 0.01926 | 0.0 | 3.38 -Other | | 0.001623 | | | 0.28 - -Nlocal: 501 ave 513 max 481 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 6556.5 ave 6608 max 6514 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Neighs: 177021 ave 182259 max 172089 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 708083 -Ave neighs/atom = 353.335 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 7 -Dangerous builds = 0 - -fix 2 all colvars peptide.colvars input out.colvars.state output out2 -colvars: Resetting the Collective Variables module. - -run 100 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 4312 960 -colvars: Creating proxy instance -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. -colvars: Using LAMMPS interface, version 2018-08-29. -colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "peptide.colvars": -colvars: # smp = on [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "one" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "two" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = "h_pot" -colvars: # colvars = { one, two } -colvars: # outputEnergy = off [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 100 -colvars: # targetForceConstant = -1 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module (re)initialized. -colvars: ---------------------------------------------------------------------- -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1. -colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1. -colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "out.colvars.state". -colvars: Restarting collective variable "one" from value: 10.0128 -colvars: Restarting collective variable "two" from value: 9.62236 -colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out2.colvars.state". -colvars: Writing to colvar trajectory file "out2.colvars.traj". -colvars: Setting initial step number from LAMMPS: 200 -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: Performing analysis. -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.81266e-06 - 6 0.997 7.79424e-07 - 8 1.08 1.08903e-06 - 10 1.111 2.96503e-07 - 12 1.08 4.69038e-07 - 14 0.960001 0 - 18 0.957201 3.76471e-06 - 31 104.52 0.000411055 -Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond f_2 - 200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572 - 210 253.15304 -5538.5615 -6557.0215 1018.46 -6672.0498 37.676621 0.61219486 - 220 245.19621 -5522.5189 -6508.9678 986.44888 -6628.1898 36.657688 0.048643368 - 230 258.69885 -5495.7276 -6536.4989 1040.7713 -6658.2887 34.857911 0.22092541 - 240 260.79635 -5469.8677 -6519.0775 1049.2098 -6624.18 31.576952 3.7574818 - 250 269.07527 -5438.3947 -6520.9115 1082.5167 -6616.4384 25.447674 8.6600013 - 260 266.0105 -5397.3486 -6467.5354 1070.1868 -6580.2898 26.871917 8.3323096 - 270 272.81314 -5350.8819 -6448.4364 1097.5545 -6563.823 23.114195 10.973131 - 280 279.42263 -5307.9799 -6432.125 1124.1452 -6557.3367 33.644027 8.5490488 - 290 286.8517 -5260.8409 -6414.874 1154.0331 -6515.6797 28.574839 5.9100135 -SHAKE stats (type/ave/delta) on step 300 - 4 1.111 1.79792e-05 - 6 0.997005 1.02512e-05 - 8 1.08 1.85102e-05 - 10 1.111 9.98838e-06 - 12 1.08 8.84113e-06 - 14 0.960008 0 - 18 0.957203 1.8445e-05 - 31 104.52 0.00168382 - 300 291.52794 -5216.2881 -6389.1342 1172.846 -6503.1276 27.889153 2.248246 -colvars: Saving collective variables state to "out2.colvars.state". -Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms - -Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 timesteps/s -99.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.41044 | 0.41882 | 0.42773 | 1.1 | 71.60 -Bond | 0.00056911 | 0.0011486 | 0.0018017 | 1.4 | 0.20 -Kspace | 0.056211 | 0.064277 | 0.072168 | 2.7 | 10.99 -Neigh | 0.064606 | 0.064613 | 0.064617 | 0.0 | 11.05 -Comm | 0.013311 | 0.013966 | 0.015175 | 0.6 | 2.39 -Output | 0.00027871 | 0.00051689 | 0.0012221 | 0.0 | 0.09 -Modify | 0.019776 | 0.0199 | 0.020015 | 0.1 | 3.40 -Other | | 0.001705 | | | 0.29 - -Nlocal: 501 ave 513 max 472 min -Histogram: 1 0 0 0 0 0 0 0 0 3 -Nghost: 6612.75 ave 6681 max 6561 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Neighs: 177038 ave 180136 max 170218 min -Histogram: 1 0 0 0 0 0 0 1 0 2 - -Total # of neighbors = 708152 -Ave neighs/atom = 353.369 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 8 -Dangerous builds = 0 - -colvars: Resetting the Collective Variables module. - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.1 deleted file mode 100644 index df7aca475f..0000000000 --- a/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.1 +++ /dev/null @@ -1,260 +0,0 @@ -LAMMPS (27 Nov 2018) - 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 - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 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 - reading bonds ... - 1365 bonds - reading angles ... - 786 angles - reading dihedrals ... - 207 dihedrals - reading impropers ... - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -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 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#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 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 10648 3375 -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/newton - bin: standard -colvars: Creating proxy instance -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. -colvars: Using LAMMPS interface, version 2018-08-29. -colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "peptide.colvars2": -colvars: # smp = on [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "one" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = "h_pot" -colvars: # colvars = { one } -colvars: # outputEnergy = off [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] -colvars: # centers = { 10 } -colvars: # targetCenters = { 10 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 100 -colvars: # targetForceConstant = -1 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module (re)initialized. -colvars: ---------------------------------------------------------------------- -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4. -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "peptide2.colvars.state". -colvars: Writing to colvar trajectory file "peptide2.colvars.traj". -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. -colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035. -colvars: Performing analysis. -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 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) on step 100 - 4 1.11096 0.000191462 - 6 0.996989 3.55508e-05 - 8 1.08 9.0997e-06 - 10 1.111 1.58544e-05 - 12 1.08 5.80604e-06 - 14 0.959997 0 - 18 0.957198 2.92445e-05 - 31 104.52 0.00239923 - 100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487 -colvars: Saving collective variables state to "peptide2.colvars.state". -Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms - -Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46 -Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14 -Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72 -Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90 -Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62 -Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01 -Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08 -Other | | 0.001465 | | | 0.06 - -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 = 353.41 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 13 -Dangerous builds = 1 -colvars: Resetting the Collective Variables module. - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:02 diff --git a/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.4 deleted file mode 100644 index b1916fda17..0000000000 --- a/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.4 +++ /dev/null @@ -1,260 +0,0 @@ -LAMMPS (27 Nov 2018) - 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 - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 2 by 2 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 - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -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 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#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 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 4312 960 -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/newton - bin: standard -colvars: Creating proxy instance -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is available. -colvars: Using LAMMPS interface, version 2018-08-29. -colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "peptide.colvars2": -colvars: # smp = on [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # scriptedColvarForces = off [default] -colvars: # scriptingAfterBiases = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = "one" -colvars: Initializing a new "distance" 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 "group1". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: Initializing atom group "group2". -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 , 0 , 0 ) [default] -colvars: # enableForces = on [default] -colvars: # enableFitGradients = on [default] -colvars: # printAtomIDs = off [default] -colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0. -colvars: # oneSiteSystemForce = off [default] -colvars: # oneSiteTotalForce = off [default] -colvars: All components initialized. -colvars: # timeStepFactor = 1 [default] -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [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: # runAve = off [default] -colvars: # corrFunc = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = "h_pot" -colvars: # colvars = { one } -colvars: # outputEnergy = off [default] -colvars: # timeStepFactor = 1 [default] -colvars: # writeTISamples = off [default] -colvars: # writeTIPMF = off [default] -colvars: # centers = { 10 } -colvars: # targetCenters = { 10 } [default] -colvars: # outputCenters = off [default] -colvars: # forceConstant = 100 -colvars: # targetForceConstant = -1 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module (re)initialized. -colvars: ---------------------------------------------------------------------- -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. -colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4. -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "peptide2.colvars.state". -colvars: Writing to colvar trajectory file "peptide2.colvars.traj". -colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. -colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035. -colvars: Performing analysis. -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 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) on step 100 - 4 1.11096 0.000191462 - 6 0.996989 3.55508e-05 - 8 1.08 9.0997e-06 - 10 1.111 1.58544e-05 - 12 1.08 5.80604e-06 - 14 0.959997 0 - 18 0.957198 2.92445e-05 - 31 104.52 0.00239923 - 100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487 -colvars: Saving collective variables state to "peptide2.colvars.state". -Loop time of 0.629325 on 4 procs for 100 steps with 2004 atoms - -Performance: 27.458 ns/day, 0.874 hours/ns, 158.900 timesteps/s -99.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.4012 | 0.41532 | 0.42829 | 1.9 | 65.99 -Bond | 0.0005219 | 0.0011545 | 0.0018291 | 1.8 | 0.18 -Kspace | 0.059271 | 0.071301 | 0.084393 | 4.4 | 11.33 -Neigh | 0.10416 | 0.10419 | 0.10424 | 0.0 | 16.56 -Comm | 0.015643 | 0.016628 | 0.017256 | 0.5 | 2.64 -Output | 0.00025177 | 0.00033599 | 0.00058722 | 0.0 | 0.05 -Modify | 0.01912 | 0.019129 | 0.019141 | 0.0 | 3.04 -Other | | 0.001264 | | | 0.20 - -Nlocal: 501 ave 513 max 494 min -Histogram: 1 1 0 1 0 0 0 0 0 1 -Nghost: 6572.5 ave 6593 max 6548 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 177058 ave 181778 max 174301 min -Histogram: 2 0 0 0 1 0 0 0 0 1 - -Total # of neighbors = 708234 -Ave neighs/atom = 353.41 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 13 -Dangerous builds = 1 -colvars: Resetting the Collective Variables module. - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.1 deleted file mode 100644 index a6801fe306..0000000000 --- a/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.1 +++ /dev/null @@ -1,163 +0,0 @@ -LAMMPS (27 Nov 2018) - 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 - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 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 - reading bonds ... - 1365 bonds - reading angles ... - 786 angles - reading dihedrals ... - 207 dihedrals - reading impropers ... - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -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 - -fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0 -fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0 - -fix 2a ref setforce 0.0 0.0 0.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -variable sp equal f_3a+f_3b - -thermo_style custom step temp etotal pe ke epair ebond v_sp -thermo 10 - - -run 100 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 10648 3375 -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/newton - bin: standard -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond v_sp - 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 - 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 - 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 - 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 - 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 - 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 - 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 - 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 - 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 - 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97155e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84253e-05 - 12 1.08 7.2713e-06 - 14 0.959996 0 - 18 0.957198 3.36079e-05 - 31 104.52 0.0030599 - 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 -Loop time of 2.21146 on 1 procs for 100 steps with 2004 atoms - -Performance: 7.814 ns/day, 3.071 hours/ns, 45.219 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.6195 | 1.6195 | 1.6195 | 0.0 | 73.23 -Bond | 0.0033534 | 0.0033534 | 0.0033534 | 0.0 | 0.15 -Kspace | 0.17464 | 0.17464 | 0.17464 | 0.0 | 7.90 -Neigh | 0.37337 | 0.37337 | 0.37337 | 0.0 | 16.88 -Comm | 0.013891 | 0.013891 | 0.013891 | 0.0 | 0.63 -Output | 0.00037336 | 0.00037336 | 0.00037336 | 0.0 | 0.02 -Modify | 0.024753 | 0.024753 | 0.024753 | 0.0 | 1.12 -Other | | 0.001613 | | | 0.07 - -Nlocal: 2004 ave 2004 max 2004 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11124 ave 11124 max 11124 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 708237 ave 708237 max 708237 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 708237 -Ave neighs/atom = 353.412 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 12 -Dangerous builds = 2 -Total wall time: 0:00:02 diff --git a/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.4 deleted file mode 100644 index 025c371640..0000000000 --- a/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.4 +++ /dev/null @@ -1,163 +0,0 @@ -LAMMPS (27 Nov 2018) - 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 - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 2 by 2 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 - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -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 - -fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0 -fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0 - -fix 2a ref setforce 0.0 0.0 0.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -variable sp equal f_3a+f_3b - -thermo_style custom step temp etotal pe ke epair ebond v_sp -thermo 10 - - -run 100 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 4312 960 -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/newton - bin: standard -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond v_sp - 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 - 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 - 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 - 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 - 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 - 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 - 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 - 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 - 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 - 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97155e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84253e-05 - 12 1.08 7.2713e-06 - 14 0.959996 0 - 18 0.957198 3.36079e-05 - 31 104.52 0.0030599 - 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 -Loop time of 0.620672 on 4 procs for 100 steps with 2004 atoms - -Performance: 27.841 ns/day, 0.862 hours/ns, 161.116 timesteps/s -99.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.4029 | 0.41752 | 0.4307 | 1.7 | 67.27 -Bond | 0.00054789 | 0.0011698 | 0.0018225 | 1.8 | 0.19 -Kspace | 0.055853 | 0.069798 | 0.083975 | 4.3 | 11.25 -Neigh | 0.096553 | 0.096622 | 0.096707 | 0.0 | 15.57 -Comm | 0.015383 | 0.016022 | 0.01632 | 0.3 | 2.58 -Output | 0.00033116 | 0.00057495 | 0.0012989 | 0.0 | 0.09 -Modify | 0.017549 | 0.017693 | 0.017826 | 0.1 | 2.85 -Other | | 0.001274 | | | 0.21 - -Nlocal: 501 ave 513 max 489 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Nghost: 6563.25 ave 6596 max 6519 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 177059 ave 181742 max 172942 min -Histogram: 1 0 1 0 0 0 1 0 0 1 - -Total # of neighbors = 708237 -Ave neighs/atom = 353.412 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 12 -Dangerous builds = 2 -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.1 deleted file mode 100644 index 7397c5475d..0000000000 --- a/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.1 +++ /dev/null @@ -1,158 +0,0 @@ -LAMMPS (27 Nov 2018) - 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 - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 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 - reading bonds ... - 1365 bonds - reading angles ... - 786 angles - reading dihedrals ... - 207 dihedrals - reading impropers ... - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -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 - -fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_3 -thermo 10 - - -run 100 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 10648 3375 -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/newton - bin: standard -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond f_3 - 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) on step 100 - 4 1.11096 0.000191462 - 6 0.996989 3.55508e-05 - 8 1.08 9.0997e-06 - 10 1.111 1.58544e-05 - 12 1.08 5.80604e-06 - 14 0.959997 0 - 18 0.957198 2.92445e-05 - 31 104.52 0.00239923 - 100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487 -Loop time of 2.2037 on 1 procs for 100 steps with 2004 atoms - -Performance: 7.841 ns/day, 3.061 hours/ns, 45.378 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.5852 | 1.5852 | 1.5852 | 0.0 | 71.93 -Bond | 0.0032725 | 0.0032725 | 0.0032725 | 0.0 | 0.15 -Kspace | 0.17308 | 0.17308 | 0.17308 | 0.0 | 7.85 -Neigh | 0.4027 | 0.4027 | 0.4027 | 0.0 | 18.27 -Comm | 0.014041 | 0.014041 | 0.014041 | 0.0 | 0.64 -Output | 0.00032306 | 0.00032306 | 0.00032306 | 0.0 | 0.01 -Modify | 0.023546 | 0.023546 | 0.023546 | 0.0 | 1.07 -Other | | 0.001546 | | | 0.07 - -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 = 353.41 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 13 -Dangerous builds = 1 -Total wall time: 0:00:02 diff --git a/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.4 deleted file mode 100644 index 0e3f0d3b6b..0000000000 --- a/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.4 +++ /dev/null @@ -1,158 +0,0 @@ -LAMMPS (27 Nov 2018) - 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 - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 2 by 2 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 - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -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 - -fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_3 -thermo 10 - - -run 100 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:321) - 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 = 4312 960 -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/newton - bin: standard -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond f_3 - 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) on step 100 - 4 1.11096 0.000191462 - 6 0.996989 3.55508e-05 - 8 1.08 9.0997e-06 - 10 1.111 1.58544e-05 - 12 1.08 5.80604e-06 - 14 0.959997 0 - 18 0.957198 2.92445e-05 - 31 104.52 0.00239923 - 100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487 -Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms - -Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s -99.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.40372 | 0.41244 | 0.41714 | 0.8 | 66.95 -Bond | 0.00053573 | 0.0011384 | 0.0017946 | 1.8 | 0.18 -Kspace | 0.060087 | 0.063993 | 0.07306 | 2.1 | 10.39 -Neigh | 0.1033 | 0.10349 | 0.1036 | 0.0 | 16.80 -Comm | 0.01568 | 0.016453 | 0.017178 | 0.5 | 2.67 -Output | 0.00028253 | 0.00032026 | 0.00043178 | 0.0 | 0.05 -Modify | 0.016238 | 0.016955 | 0.017704 | 0.5 | 2.75 -Other | | 0.001239 | | | 0.20 - -Nlocal: 501 ave 513 max 494 min -Histogram: 1 1 0 1 0 0 0 0 0 1 -Nghost: 6572.5 ave 6593 max 6548 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 177058 ave 181778 max 174301 min -Histogram: 2 0 0 0 1 0 0 0 0 1 - -Total # of neighbors = 708234 -Ave neighs/atom = 353.41 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 13 -Dangerous builds = 1 -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1 b/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1 new file mode 100644 index 0000000000..0b8522c55f --- /dev/null +++ b/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1 @@ -0,0 +1,732 @@ +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 out*.colvars.*" +fix 2 all colvars peptide.colvars +---------------------------------------------------------------------- +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 2a ref setforce 0.0 0.0 0.0 + +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.colvar.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.colvars": +# 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 1 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] +---------------------------------------------------------------------- + Initializing a new collective variable. + # name = "two" + 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 1 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, 2 in total. +---------------------------------------------------------------------- + Initializing a new "harmonic" instance. + # name = "h_pot" + # colvars = { one, two } + # stepZeroData = off [default] + # outputEnergy = off [default] + # outputFreq = 1000 [default] + # timeStepFactor = 1 [default] + # writeTISamples = off [default] + # writeTIPMF = off [default] + # centers = { 10, 10 } + # targetCenters = { 10, 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). + The force constant for colvar "two" 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. 1 atoms: total mass = 12.011, total charge = 0.51. +Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16. +Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51. +The final output state file will be "out.colvars.state". +Synchronizing (emptying the buffer of) trajectory file "out.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 292.14604 + 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 + 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 + 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 + 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 + 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 + 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 + 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 + 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 + 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 +SHAKE stats (type/ave/delta/count) on step 100 +Bond: 4 1.11098 8.97155e-05 9 +Bond: 6 0.996996 1.00568e-05 6 +Bond: 8 1.08 6.02345e-06 7 +Bond: 10 1.111 1.84253e-05 8 +Bond: 12 1.08 7.2713e-06 9 +Bond: 14 0.959996 0 1 +Bond: 18 0.957198 3.36079e-05 1280 +Angle: 31 104.52 0.0030599 640 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 +Saving collective variables state to "out.colvars.state". +Loop time of 0.897199 on 1 procs for 100 steps with 2004 atoms + +Performance: 19.260 ns/day, 1.246 hours/ns, 111.458 timesteps/s, 223.362 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 | 0.71298 | 0.71298 | 0.71298 | 0.0 | 79.47 +Bond | 0.001284 | 0.001284 | 0.001284 | 0.0 | 0.14 +Kspace | 0.041232 | 0.041232 | 0.041232 | 0.0 | 4.60 +Neigh | 0.1277 | 0.1277 | 0.1277 | 0.0 | 14.23 +Comm | 0.0033285 | 0.0033285 | 0.0033285 | 0.0 | 0.37 +Output | 0.00017467 | 0.00017467 | 0.00017467 | 0.0 | 0.02 +Modify | 0.010003 | 0.010003 | 0.010003 | 0.0 | 1.11 +Other | | 0.0004941 | | | 0.06 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11124 ave 11124 max 11124 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708237 ave 708237 max 708237 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 708237 +Ave neighs/atom = 353.41168 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 12 +Dangerous builds = 2 + +run 100 + +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 + +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 +Current simulation parameters: initial step = 100, 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. 1 atoms: total mass = 12.011, total charge = 0.51. +Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16. +Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51. +SHAKE stats (type/ave/delta/count) on step 100 +Bond: 4 1.11098 8.97155e-05 9 +Bond: 6 0.996996 1.00568e-05 6 +Bond: 8 1.08 6.02345e-06 7 +Bond: 10 1.111 1.84253e-05 8 +Bond: 12 1.08 7.2713e-06 9 +Bond: 14 0.959996 0 1 +Bond: 18 0.957198 3.36079e-05 1280 +Angle: 31 104.52 0.0030599 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 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 + 110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657 + 120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812 + 130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591 + 140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517 + 150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008 + 160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1372 19.717399 12.339679 + 170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217 + 180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4236 26.200127 3.4336037 + 190 250.80862 -5555.2554 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286 +SHAKE stats (type/ave/delta/count) on step 200 +Bond: 4 1.111 1.81266e-06 9 +Bond: 6 0.997 7.79424e-07 6 +Bond: 8 1.08 1.08903e-06 7 +Bond: 10 1.111 2.96503e-07 8 +Bond: 12 1.08 4.69038e-07 9 +Bond: 14 0.960001 0 1 +Bond: 18 0.957201 3.76471e-06 1280 +Angle: 31 104.52 0.000411055 640 + 200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572 +Saving collective variables state to "out.colvars.state". +Loop time of 0.855092 on 1 procs for 100 steps with 2004 atoms + +Performance: 20.208 ns/day, 1.188 hours/ns, 116.946 timesteps/s, 234.361 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 | 0.71954 | 0.71954 | 0.71954 | 0.0 | 84.15 +Bond | 0.0012655 | 0.0012655 | 0.0012655 | 0.0 | 0.15 +Kspace | 0.042826 | 0.042826 | 0.042826 | 0.0 | 5.01 +Neigh | 0.078128 | 0.078128 | 0.078128 | 0.0 | 9.14 +Comm | 0.0029003 | 0.0029003 | 0.0029003 | 0.0 | 0.34 +Output | 0.00016605 | 0.00016605 | 0.00016605 | 0.0 | 0.02 +Modify | 0.0097753 | 0.0097753 | 0.0097753 | 0.0 | 1.14 +Other | | 0.0004882 | | | 0.06 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11159 ave 11159 max 11159 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708083 ave 708083 max 708083 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 708083 +Ave neighs/atom = 353.33483 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 7 +Dangerous builds = 0 + +fix 2 all colvars peptide.colvars input out.colvars.state output out2 +---------------------------------------------------------------------- +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". +Setting initial step number from MD engine: 200 + +run 100 +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 +Will read input state from file "out.colvars.state"---------------------------------------------------------------------- +Reading new configuration from file "peptide.colvars": +# 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 1 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] +---------------------------------------------------------------------- + Initializing a new collective variable. + # name = "two" + 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 1 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, 2 in total. +---------------------------------------------------------------------- + Initializing a new "harmonic" instance. + # name = "h_pot" + # colvars = { one, two } + # stepZeroData = off [default] + # outputEnergy = off [default] + # outputFreq = 1000 [default] + # timeStepFactor = 1 [default] + # writeTISamples = off [default] + # writeTIPMF = off [default] + # centers = { 10, 10 } + # targetCenters = { 10, 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). + The force constant for colvar "two" 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 = 200, 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. 1 atoms: total mass = 12.011, total charge = 0.51. +Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16. +Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51. +---------------------------------------------------------------------- +Loading state from text file "out.colvars.state". + Restarting collective variable "one" from value: 10.0128 + Restarting collective variable "two" from value: 9.62236 + Restarted harmonic bias "h_pot" with step number 200. +---------------------------------------------------------------------- +The final output state file will be "out2.colvars.state". +SHAKE stats (type/ave/delta/count) on step 200 +Bond: 4 1.111 1.81266e-06 9 +Bond: 6 0.997 7.79424e-07 6 +Bond: 8 1.08 1.08903e-06 7 +Bond: 10 1.111 2.96503e-07 8 +Bond: 12 1.08 4.69038e-07 9 +Bond: 14 0.960001 0 1 +Bond: 18 0.957201 3.76471e-06 1280 +Angle: 31 104.52 0.000411055 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 + 200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572 + 210 253.15302 -5538.5614 -6557.0213 1018.4599 -6672.0496 37.676621 0.61219488 + 220 245.19621 -5522.5192 -6508.9681 986.44887 -6628.19 36.657688 0.048643387 + 230 258.69885 -5495.7277 -6536.499 1040.7713 -6658.2888 34.857911 0.2209256 + 240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.1799 31.576952 3.7574815 + 250 269.07527 -5438.3947 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600023 + 260 266.01046 -5397.3484 -6467.5351 1070.1867 -6580.2895 26.871919 8.3323102 + 270 272.81307 -5350.882 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132 + 280 279.42264 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644021 8.5490492 + 290 286.85168 -5260.8411 -6414.874 1154.033 -6515.6797 28.574838 5.9100104 +SHAKE stats (type/ave/delta/count) on step 300 +Bond: 4 1.111 1.79793e-05 9 +Bond: 6 0.997005 1.02512e-05 6 +Bond: 8 1.08 1.85103e-05 7 +Bond: 10 1.111 9.9884e-06 8 +Bond: 12 1.08 8.84114e-06 9 +Bond: 14 0.960008 0 1 +Bond: 18 0.957203 1.8445e-05 1280 +Angle: 31 104.52 0.00168383 640 + 300 291.52794 -5216.288 -6389.1341 1172.846 -6503.1276 27.889149 2.2482427 +Saving collective variables state to "out2.colvars.state". +Loop time of 0.86889 on 1 procs for 100 steps with 2004 atoms + +Performance: 19.887 ns/day, 1.207 hours/ns, 115.089 timesteps/s, 230.639 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 | 0.72728 | 0.72728 | 0.72728 | 0.0 | 83.70 +Bond | 0.0012755 | 0.0012755 | 0.0012755 | 0.0 | 0.15 +Kspace | 0.041631 | 0.041631 | 0.041631 | 0.0 | 4.79 +Neigh | 0.085283 | 0.085283 | 0.085283 | 0.0 | 9.82 +Comm | 0.0029986 | 0.0029986 | 0.0029986 | 0.0 | 0.35 +Output | 0.00013272 | 0.00013272 | 0.00013272 | 0.0 | 0.02 +Modify | 0.0097972 | 0.0097972 | 0.0097972 | 0.0 | 1.13 +Other | | 0.0004882 | | | 0.06 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11296 ave 11296 max 11296 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708152 ave 708152 max 708152 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 708152 +Ave neighs/atom = 353.36926 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 8 +Dangerous builds = 0 + +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4 b/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4 new file mode 100644 index 0000000000..b45cb03f96 --- /dev/null +++ b/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4 @@ -0,0 +1,732 @@ +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 2 by 2 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 2 by 2 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 = 0.011 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 out*.colvars.*" +fix 2 all colvars peptide.colvars +---------------------------------------------------------------------- +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 2a ref setforce 0.0 0.0 0.0 + +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.colvar.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 = 4312 960 +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.colvars": +# 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 1 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] +---------------------------------------------------------------------- + Initializing a new collective variable. + # name = "two" + 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 1 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, 2 in total. +---------------------------------------------------------------------- + Initializing a new "harmonic" instance. + # name = "h_pot" + # colvars = { one, two } + # stepZeroData = off [default] + # outputEnergy = off [default] + # outputFreq = 1000 [default] + # timeStepFactor = 1 [default] + # writeTISamples = off [default] + # writeTIPMF = off [default] + # centers = { 10, 10 } + # targetCenters = { 10, 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). + The force constant for colvar "two" 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. 1 atoms: total mass = 12.011, total charge = 0.51. +Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16. +Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51. +The final output state file will be "out.colvars.state". +Synchronizing (emptying the buffer of) trajectory file "out.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) = 16.02 | 16.22 | 16.41 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 292.14604 + 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 + 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 + 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 + 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 + 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 + 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 + 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 + 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 + 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 +SHAKE stats (type/ave/delta/count) on step 100 +Bond: 4 1.11098 8.97155e-05 9 +Bond: 6 0.996996 1.00568e-05 6 +Bond: 8 1.08 6.02345e-06 7 +Bond: 10 1.111 1.84253e-05 8 +Bond: 12 1.08 7.2713e-06 9 +Bond: 14 0.959996 0 1 +Bond: 18 0.957198 3.36079e-05 1280 +Angle: 31 104.52 0.0030599 640 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 +Saving collective variables state to "out.colvars.state". +Loop time of 0.246405 on 4 procs for 100 steps with 2004 atoms + +Performance: 70.128 ns/day, 0.342 hours/ns, 405.836 timesteps/s, 813.295 katom-step/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17765 | 0.18092 | 0.18373 | 0.6 | 73.42 +Bond | 0.00021581 | 0.00045219 | 0.00069916 | 0.0 | 0.18 +Kspace | 0.018035 | 0.020459 | 0.023812 | 1.7 | 8.30 +Neigh | 0.032165 | 0.032193 | 0.032207 | 0.0 | 13.07 +Comm | 0.00566 | 0.0058533 | 0.0060088 | 0.2 | 2.38 +Output | 0.00012205 | 0.00014069 | 0.00019404 | 0.0 | 0.06 +Modify | 0.0059979 | 0.0060225 | 0.0060368 | 0.0 | 2.44 +Other | | 0.0003631 | | | 0.15 + +Nlocal: 501 ave 513 max 489 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 6563.25 ave 6596 max 6519 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 177059 ave 181742 max 172942 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 708237 +Ave neighs/atom = 353.41168 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 12 +Dangerous builds = 2 + +run 100 + +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 + +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 = 4312 960 +Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule +Current simulation parameters: initial step = 100, 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. 1 atoms: total mass = 12.011, total charge = 0.51. +Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16. +Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51. +SHAKE stats (type/ave/delta/count) on step 100 +Bond: 4 1.11098 8.97155e-05 9 +Bond: 6 0.996996 1.00568e-05 6 +Bond: 8 1.08 6.02345e-06 7 +Bond: 10 1.111 1.84253e-05 8 +Bond: 12 1.08 7.2713e-06 9 +Bond: 14 0.959996 0 1 +Bond: 18 0.957198 3.36079e-05 1280 +Angle: 31 104.52 0.0030599 640 +Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes + Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 + 110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657 + 120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812 + 130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591 + 140 253.85111 -5452.1837 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517 + 150 261.31816 -5490.4726 -6541.7816 1051.3091 -6646.6075 16.258823 6.9051008 + 160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679 + 170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217 + 180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4235 26.200127 3.4336036 + 190 250.80862 -5555.2555 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286 +SHAKE stats (type/ave/delta/count) on step 200 +Bond: 4 1.111 1.81266e-06 9 +Bond: 6 0.997 7.79424e-07 6 +Bond: 8 1.08 1.08903e-06 7 +Bond: 10 1.111 2.96503e-07 8 +Bond: 12 1.08 4.69038e-07 9 +Bond: 14 0.960001 0 1 +Bond: 18 0.957201 3.76471e-06 1280 +Angle: 31 104.52 0.000411055 640 + 200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572 +Saving collective variables state to "out.colvars.state". +Loop time of 0.238087 on 4 procs for 100 steps with 2004 atoms + +Performance: 72.578 ns/day, 0.331 hours/ns, 420.014 timesteps/s, 841.709 katom-step/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17913 | 0.18408 | 0.19082 | 1.1 | 77.32 +Bond | 0.00019617 | 0.00044139 | 0.00071286 | 0.0 | 0.19 +Kspace | 0.016186 | 0.022449 | 0.02737 | 3.0 | 9.43 +Neigh | 0.018728 | 0.018753 | 0.018777 | 0.0 | 7.88 +Comm | 0.0052171 | 0.0055397 | 0.0058422 | 0.3 | 2.33 +Output | 0.00012326 | 0.00014453 | 0.00020506 | 0.0 | 0.06 +Modify | 0.0062505 | 0.0062725 | 0.0062944 | 0.0 | 2.63 +Other | | 0.0004069 | | | 0.17 + +Nlocal: 501 ave 513 max 481 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 6556.5 ave 6608 max 6514 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 177021 ave 182259 max 172089 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 708083 +Ave neighs/atom = 353.33483 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 7 +Dangerous builds = 0 + +fix 2 all colvars peptide.colvars input out.colvars.state output out2 +---------------------------------------------------------------------- +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". +Setting initial step number from MD engine: 200 + +run 100 +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 = 4312 960 +Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule +Will read input state from file "out.colvars.state"---------------------------------------------------------------------- +Reading new configuration from file "peptide.colvars": +# 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 1 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] +---------------------------------------------------------------------- + Initializing a new collective variable. + # name = "two" + 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 1 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, 2 in total. +---------------------------------------------------------------------- + Initializing a new "harmonic" instance. + # name = "h_pot" + # colvars = { one, two } + # stepZeroData = off [default] + # outputEnergy = off [default] + # outputFreq = 1000 [default] + # timeStepFactor = 1 [default] + # writeTISamples = off [default] + # writeTIPMF = off [default] + # centers = { 10, 10 } + # targetCenters = { 10, 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). + The force constant for colvar "two" 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 = 200, 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. 1 atoms: total mass = 12.011, total charge = 0.51. +Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16. +Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51. +---------------------------------------------------------------------- +Loading state from text file "out.colvars.state". + Restarting collective variable "one" from value: 10.0128 + Restarting collective variable "two" from value: 9.62236 + Restarted harmonic bias "h_pot" with step number 200. +---------------------------------------------------------------------- +The final output state file will be "out2.colvars.state". +SHAKE stats (type/ave/delta/count) on step 200 +Bond: 4 1.111 1.81266e-06 9 +Bond: 6 0.997 7.79424e-07 6 +Bond: 8 1.08 1.08903e-06 7 +Bond: 10 1.111 2.96503e-07 8 +Bond: 12 1.08 4.69038e-07 9 +Bond: 14 0.960001 0 1 +Bond: 18 0.957201 3.76471e-06 1280 +Angle: 31 104.52 0.000411055 640 +Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes + Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572 + 210 253.15302 -5538.5615 -6557.0215 1018.4599 -6672.0498 37.676621 0.61219488 + 220 245.19621 -5522.5191 -6508.9679 986.44887 -6628.1899 36.657688 0.048643387 + 230 258.69885 -5495.7275 -6536.4989 1040.7713 -6658.2886 34.857911 0.22092559 + 240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.18 31.576952 3.7574815 + 250 269.07527 -5438.3946 -6520.9113 1082.5167 -6616.4382 25.447675 8.6600023 + 260 266.01046 -5397.3485 -6467.5352 1070.1867 -6580.2896 26.871919 8.3323104 + 270 272.81307 -5350.8819 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132 + 280 279.42265 -5307.9799 -6432.1251 1124.1452 -6557.3368 33.644022 8.5490489 + 290 286.85168 -5260.841 -6414.874 1154.033 -6515.6797 28.574838 5.9100102 +SHAKE stats (type/ave/delta/count) on step 300 +Bond: 4 1.111 1.79793e-05 9 +Bond: 6 0.997005 1.02512e-05 6 +Bond: 8 1.08 1.85103e-05 7 +Bond: 10 1.111 9.9884e-06 8 +Bond: 12 1.08 8.84114e-06 9 +Bond: 14 0.960008 0 1 +Bond: 18 0.957203 1.8445e-05 1280 +Angle: 31 104.52 0.00168383 640 + 300 291.52793 -5216.288 -6389.1341 1172.846 -6503.1275 27.88915 2.2482428 +Saving collective variables state to "out2.colvars.state". +Loop time of 0.245933 on 4 procs for 100 steps with 2004 atoms + +Performance: 70.263 ns/day, 0.342 hours/ns, 406.614 timesteps/s, 814.854 katom-step/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17862 | 0.18666 | 0.19126 | 1.2 | 75.90 +Bond | 0.00021974 | 0.00048505 | 0.00077708 | 0.0 | 0.20 +Kspace | 0.018338 | 0.02317 | 0.031148 | 3.4 | 9.42 +Neigh | 0.022128 | 0.022183 | 0.022222 | 0.0 | 9.02 +Comm | 0.0059137 | 0.0060593 | 0.0064247 | 0.3 | 2.46 +Output | 0.00014648 | 0.00015946 | 0.00019596 | 0.0 | 0.06 +Modify | 0.0067012 | 0.00674 | 0.0067814 | 0.0 | 2.74 +Other | | 0.0004738 | | | 0.19 + +Nlocal: 501 ave 513 max 472 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 6612.75 ave 6681 max 6561 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Neighs: 177038 ave 180136 max 170218 min +Histogram: 1 0 0 0 0 0 0 1 0 2 + +Total # of neighbors = 708152 +Ave neighs/atom = 353.36926 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 8 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1 b/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1 new file mode 100644 index 0000000000..7777c152fb --- /dev/null +++ b/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1 @@ -0,0 +1,344 @@ +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 diff --git a/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4 b/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4 new file mode 100644 index 0000000000..9aa28f51d5 --- /dev/null +++ b/examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4 @@ -0,0 +1,344 @@ +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 2 by 2 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 2 by 2 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 = 0.011 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 = 4312 960 +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) = 16.02 | 16.22 | 16.41 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 0.253421 on 4 procs for 100 steps with 2004 atoms + +Performance: 68.187 ns/day, 0.352 hours/ns, 394.600 timesteps/s, 790.779 katom-step/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.1771 | 0.18185 | 0.18625 | 0.8 | 71.76 +Bond | 0.00028771 | 0.00056007 | 0.00087366 | 0.0 | 0.22 +Kspace | 0.017434 | 0.021451 | 0.026345 | 2.4 | 8.46 +Neigh | 0.035481 | 0.035495 | 0.035512 | 0.0 | 14.01 +Comm | 0.0064003 | 0.0065098 | 0.0065994 | 0.1 | 2.57 +Output | 0.00012417 | 0.00013888 | 0.00018109 | 0.0 | 0.05 +Modify | 0.0069389 | 0.0069521 | 0.0069617 | 0.0 | 2.74 +Other | | 0.0004667 | | | 0.18 + +Nlocal: 501 ave 513 max 494 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 6572.5 ave 6593 max 6548 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 177058 ave 181778 max 174301 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +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 diff --git a/examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1 b/examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1 new file mode 100644 index 0000000000..322fac3afa --- /dev/null +++ b/examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1 @@ -0,0 +1,194 @@ +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 + +fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0 +fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0 + +fix 2a ref setforce 0.0 0.0 0.0 + +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.spring.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +variable sp equal f_3a+f_3b + +thermo_style custom step temp etotal pe ke epair ebond v_sp +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 +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 v_sp + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 + 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 + 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 + 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 + 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 + 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 + 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 + 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 + 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 + 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 +SHAKE stats (type/ave/delta/count) on step 100 +Bond: 4 1.11098 8.97155e-05 9 +Bond: 6 0.996996 1.00568e-05 6 +Bond: 8 1.08 6.02345e-06 7 +Bond: 10 1.111 1.84253e-05 8 +Bond: 12 1.08 7.2713e-06 9 +Bond: 14 0.959996 0 1 +Bond: 18 0.957198 3.36079e-05 1280 +Angle: 31 104.52 0.0030599 640 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 +Loop time of 0.893963 on 1 procs for 100 steps with 2004 atoms + +Performance: 19.330 ns/day, 1.242 hours/ns, 111.861 timesteps/s, 224.170 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 | 0.7114 | 0.7114 | 0.7114 | 0.0 | 79.58 +Bond | 0.0012663 | 0.0012663 | 0.0012663 | 0.0 | 0.14 +Kspace | 0.041962 | 0.041962 | 0.041962 | 0.0 | 4.69 +Neigh | 0.12542 | 0.12542 | 0.12542 | 0.0 | 14.03 +Comm | 0.0033466 | 0.0033466 | 0.0033466 | 0.0 | 0.37 +Output | 0.00017765 | 0.00017765 | 0.00017765 | 0.0 | 0.02 +Modify | 0.0098927 | 0.0098927 | 0.0098927 | 0.0 | 1.11 +Other | | 0.0005014 | | | 0.06 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11124 ave 11124 max 11124 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708237 ave 708237 max 708237 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 708237 +Ave neighs/atom = 353.41168 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 12 +Dangerous builds = 2 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4 b/examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4 new file mode 100644 index 0000000000..1affba784a --- /dev/null +++ b/examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4 @@ -0,0 +1,194 @@ +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 2 by 2 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 2 by 2 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 = 0.010 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 + +fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0 +fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0 + +fix 2a ref setforce 0.0 0.0 0.0 + +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.spring.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +variable sp equal f_3a+f_3b + +thermo_style custom step temp etotal pe ke epair ebond v_sp +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 = 4312 960 +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 +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) = 16.01 | 16.22 | 16.41 Mbytes + Step Temp TotEng PotEng KinEng E_pair E_bond v_sp + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 + 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 + 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 + 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 + 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 + 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 + 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 + 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 + 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 + 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 +SHAKE stats (type/ave/delta/count) on step 100 +Bond: 4 1.11098 8.97155e-05 9 +Bond: 6 0.996996 1.00568e-05 6 +Bond: 8 1.08 6.02345e-06 7 +Bond: 10 1.111 1.84253e-05 8 +Bond: 12 1.08 7.2713e-06 9 +Bond: 14 0.959996 0 1 +Bond: 18 0.957198 3.36079e-05 1280 +Angle: 31 104.52 0.0030599 640 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 +Loop time of 0.247541 on 4 procs for 100 steps with 2004 atoms + +Performance: 69.806 ns/day, 0.344 hours/ns, 403.973 timesteps/s, 809.561 katom-step/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17778 | 0.18129 | 0.18529 | 0.8 | 73.24 +Bond | 0.00024025 | 0.00049912 | 0.00080235 | 0.0 | 0.20 +Kspace | 0.016204 | 0.0204 | 0.023648 | 2.3 | 8.24 +Neigh | 0.032425 | 0.032462 | 0.032496 | 0.0 | 13.11 +Comm | 0.0063955 | 0.0065509 | 0.0067449 | 0.2 | 2.65 +Output | 0.0001675 | 0.00018071 | 0.00021385 | 0.0 | 0.07 +Modify | 0.0057027 | 0.0057304 | 0.0057568 | 0.0 | 2.31 +Other | | 0.0004289 | | | 0.17 + +Nlocal: 501 ave 513 max 489 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 6563.25 ave 6596 max 6519 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 177059 ave 181742 max 172942 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 708237 +Ave neighs/atom = 353.41168 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 12 +Dangerous builds = 2 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1 b/examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1 new file mode 100644 index 0000000000..e0c5ebb710 --- /dev/null +++ b/examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1 @@ -0,0 +1,189 @@ +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 + +fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0 + +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.spring2.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +thermo_style custom step temp etotal pe ke epair ebond f_3 +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 +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_3 + 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 +Loop time of 0.910778 on 1 procs for 100 steps with 2004 atoms + +Performance: 18.973 ns/day, 1.265 hours/ns, 109.796 timesteps/s, 220.032 katom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.71746 | 0.71746 | 0.71746 | 0.0 | 78.77 +Bond | 0.0012756 | 0.0012756 | 0.0012756 | 0.0 | 0.14 +Kspace | 0.042462 | 0.042462 | 0.042462 | 0.0 | 4.66 +Neigh | 0.13497 | 0.13497 | 0.13497 | 0.0 | 14.82 +Comm | 0.0036247 | 0.0036247 | 0.0036247 | 0.0 | 0.40 +Output | 0.00016145 | 0.00016145 | 0.00016145 | 0.0 | 0.02 +Modify | 0.010258 | 0.010258 | 0.010258 | 0.0 | 1.13 +Other | | 0.0005695 | | | 0.06 + +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 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4 b/examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4 new file mode 100644 index 0000000000..5e65a6b17d --- /dev/null +++ b/examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4 @@ -0,0 +1,189 @@ +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 2 by 2 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 2 by 2 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 = 0.011 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 + +fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0 + +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.spring2.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +thermo_style custom step temp etotal pe ke epair ebond f_3 +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 = 4312 960 +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 +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) = 16.01 | 16.22 | 16.41 Mbytes + Step Temp TotEng PotEng KinEng E_pair E_bond f_3 + 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 +Loop time of 0.248812 on 4 procs for 100 steps with 2004 atoms + +Performance: 69.450 ns/day, 0.346 hours/ns, 401.910 timesteps/s, 805.428 katom-step/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17522 | 0.18002 | 0.18454 | 1.0 | 72.35 +Bond | 0.00020312 | 0.00044793 | 0.00074786 | 0.0 | 0.18 +Kspace | 0.016556 | 0.021002 | 0.026079 | 3.0 | 8.44 +Neigh | 0.035695 | 0.03571 | 0.03572 | 0.0 | 14.35 +Comm | 0.0057324 | 0.0058127 | 0.005874 | 0.1 | 2.34 +Output | 0.00013005 | 0.00013946 | 0.00016548 | 0.0 | 0.06 +Modify | 0.00526 | 0.0052645 | 0.005272 | 0.0 | 2.12 +Other | | 0.0004197 | | | 0.17 + +Nlocal: 501 ave 513 max 494 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 6572.5 ave 6593 max 6548 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 177058 ave 181778 max 174301 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 708234 +Ave neighs/atom = 353.41018 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 13 +Dangerous builds = 1 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/colvars/out.colvars.state b/examples/PACKAGES/colvars/out.colvars.state index e1c98c5096..ea803a5528 100644 --- a/examples/PACKAGES/colvars/out.colvars.state +++ b/examples/PACKAGES/colvars/out.colvars.state @@ -1,17 +1,17 @@ configuration { step 200 dt 2.000000e+00 - version 2020-07-07 + version 2024-06-04 } colvar { name one - x 1.00127732034965e+01 + x 10.012773203962 } colvar { name two - x 9.62235997490241e+00 + x 9.6223599748448 } restraint { diff --git a/examples/PACKAGES/colvars/out.colvars.state.old b/examples/PACKAGES/colvars/out.colvars.state.old index 458485ca83..4f26b0b566 100644 --- a/examples/PACKAGES/colvars/out.colvars.state.old +++ b/examples/PACKAGES/colvars/out.colvars.state.old @@ -1,17 +1,17 @@ configuration { step 100 dt 2.000000e+00 - version 2020-07-07 + version 2024-06-04 } colvar { name one - x 1.00136989326255e+01 + x 10.013698932648 } colvar { name two - x 1.00648830006091e+01 + x 10.064883000604 } restraint { diff --git a/examples/PACKAGES/colvars/out.colvars.traj b/examples/PACKAGES/colvars/out.colvars.traj index 15aa912846..4acd3b90c7 100644 --- a/examples/PACKAGES/colvars/out.colvars.traj +++ b/examples/PACKAGES/colvars/out.colvars.traj @@ -13,191 +13,191 @@ 11 1.01744058364969e+01 8.66916428851601e+00 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1.00122066751424e+01 9.63383866285097e+00 + 200 1.00127732039621e+01 9.62235997484479e+00 diff --git a/examples/PACKAGES/colvars/out2.colvars.state b/examples/PACKAGES/colvars/out2.colvars.state index 95bb3dafbb..e8e73653be 100644 --- a/examples/PACKAGES/colvars/out2.colvars.state +++ b/examples/PACKAGES/colvars/out2.colvars.state @@ -1,17 +1,17 @@ configuration { step 300 dt 2.000000e+00 - version 2020-07-07 + version 2024-06-04 } colvar { name one - x 9.95315918568411e+00 + x 9.9531592295885 } colvar { name two - x 9.79318883680258e+00 + x 9.7931889789213 } restraint { diff --git a/examples/PACKAGES/colvars/out2.colvars.traj b/examples/PACKAGES/colvars/out2.colvars.traj index 365f9b8306..e856b3a96a 100644 --- a/examples/PACKAGES/colvars/out2.colvars.traj +++ b/examples/PACKAGES/colvars/out2.colvars.traj @@ -1,102 +1,102 @@ # step one two - 200 1.00127732034965e+01 9.62235997490241e+00 - 201 1.00139198864982e+01 9.61766167925624e+00 - 202 1.00155004339120e+01 9.62284272858813e+00 - 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9.62975551670189e+00 + 287 1.00386905666453e+01 9.63733600598964e+00 + 288 1.00391292301728e+01 9.64435235461356e+00 + 289 1.00396076684883e+01 9.65114132457984e+00 + 290 1.00391967232973e+01 9.65843914091158e+00 + 291 1.00370408787737e+01 9.66713746391752e+00 + 292 1.00325613002434e+01 9.67798048381559e+00 + 293 1.00255913122523e+01 9.69130455064462e+00 + 294 1.00164043783898e+01 9.70689857240811e+00 + 295 1.00056261042358e+01 9.72399828398139e+00 + 296 9.99406220236070e+00 9.74140420689973e+00 + 297 9.98250803047048e+00 9.75776457125789e+00 + 298 9.97160203186903e+00 9.77203086770013e+00 + 299 9.96175639897897e+00 9.78379391142304e+00 + 300 9.95315922958854e+00 9.79318897892133e+00 diff --git a/examples/PACKAGES/colvars/peptide2.colvars.state b/examples/PACKAGES/colvars/peptide2.colvars.state index 6e23e3a6c5..4f57df80b7 100644 --- a/examples/PACKAGES/colvars/peptide2.colvars.state +++ b/examples/PACKAGES/colvars/peptide2.colvars.state @@ -1,12 +1,12 @@ configuration { step 100 dt 2.000000e+00 - version 2020-07-07 + version 2024-06-04 } colvar { name one - x 1.00387423506482e+01 + x 10.038742350674 } restraint { diff --git a/examples/PACKAGES/colvars/peptide2.colvars.traj b/examples/PACKAGES/colvars/peptide2.colvars.traj index 0d8931bda7..421338dbf7 100644 --- a/examples/PACKAGES/colvars/peptide2.colvars.traj +++ b/examples/PACKAGES/colvars/peptide2.colvars.traj @@ -20,16 +20,16 @@ 18 9.41602481112176e+00 19 9.44413580740584e+00 20 9.49001346044027e+00 - 21 9.55036359015270e+00 - 22 9.62258602486444e+00 - 23 9.70460545744668e+00 + 21 9.55036359015271e+00 + 22 9.62258602486445e+00 + 23 9.70460545744666e+00 24 9.79475465622561e+00 - 25 9.89135302429916e+00 - 26 9.99213332770717e+00 + 25 9.89135302429913e+00 + 26 9.99213332770716e+00 27 1.00938522423366e+01 28 1.01925371414626e+01 29 1.02845129002944e+01 - 30 1.03676671987640e+01 + 30 1.03676671987639e+01 31 1.04416385355998e+01 32 1.05071349561950e+01 33 1.05650463398331e+01 @@ -41,39 +41,39 @@ 39 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9.45286356660258e+00 64 9.52464585631223e+00 65 9.61230948096192e+00 - 66 9.71074418990813e+00 - 67 9.81507236552599e+00 - 68 9.92117974657176e+00 - 69 1.00244259961919e+01 + 66 9.71074418990814e+00 + 67 9.81507236552600e+00 + 68 9.92117974657179e+00 + 69 1.00244259961920e+01 70 1.01178306268727e+01 - 71 1.01986985644537e+01 + 71 1.01986985644538e+01 72 1.02671003889995e+01 - 73 1.03213098011429e+01 - 74 1.03597236984298e+01 + 73 1.03213098011430e+01 + 74 1.03597236984299e+01 75 1.03817789163109e+01 76 1.03880650963390e+01 77 1.03809140245635e+01 @@ -82,21 +82,21 @@ 80 1.03243676495902e+01 81 1.03082131278348e+01 82 1.02961310659179e+01 - 83 1.02862115513553e+01 + 83 1.02862115513552e+01 84 1.02756073299153e+01 85 1.02618115461408e+01 86 1.02435127550163e+01 87 1.02212112849545e+01 88 1.01972788307491e+01 - 89 1.01743918261207e+01 + 89 1.01743918261206e+01 90 1.01538328424605e+01 91 1.01363005552771e+01 - 92 1.01223066231827e+01 - 93 1.01118037967830e+01 + 92 1.01223066231826e+01 + 93 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