LAMMPS (21 May 2012-ICMS) # 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 3 = max bonds/atom 6 = max angles/atom 14 = max dihedrals/atom 1 = max impropers/atom orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) 1 by 2 by 2 MPI processor grid 2004 atoms 2004 velocities 1365 bonds 786 angles 207 dihedrals 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 ... G vector (1/distance) = 0.268721 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.01614 estimated relative force accuracy = 4.86052e-05 using single precision FFTs brick FFT buffer size/proc = 4312 960 3696 colvars: ---------------------------------------------------------------------- colvars: Initializing the collective variables module, version 2012-03-23. colvars: # analysis = off [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 1000 colvars: # colvarsTrajAppend = off [default] colvars: The restart output state file will be "rest.colvars.state". colvars: The final output state file will be "peptide2.colvars.state". colvars: The trajectory file will be "peptide2.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = one colvars: Initializing a new "distance" component. colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] colvars: # oneSiteSystemForce = off [default] colvars: Initializing atom group "group1". colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. colvars: Initializing atom group "group2". colvars: Atom group "group2" defined, 4 initialized: total mass = 15.035. colvars: All components initialized. colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 0 [default] colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] colvars: # outputSystemForce = off [default] colvars: # outputAppliedForce = 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: # forceConstant = 100 colvars: # centers = { 10 } colvars: # targetCenters = { 10 } [default] colvars: # targetForceConstant = 0 [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module initialized. colvars: ---------------------------------------------------------------------- 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 Memory usage per processor = 10.1924 Mbytes Step Temp TotEng PotEng KinEng E_pair E_bond 2 0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323 10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269 20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392 30 316.97689 -5025.5598 -6300.7896 1275.2297 -6422.5336 27.323113 6.7588863 40 297.5581 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676872 25.625156 50 296.80003 -5117.2927 -6311.3488 1194.0562 -6451.8275 30.631279 5.3320297 60 281.72797 -5188.494 -6321.9138 1133.4198 -6427.8833 26.287652 20.573959 70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742889 0.69414888 80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606437 90 270.43386 -5334.0846 -6422.067 1087.9825 -6563.2486 39.845992 1.1832495 SHAKE stats (type/ave/delta) on step 100 4 1.11096 0.000191466 6 0.996989 3.5552e-05 8 1.08 9.10001e-06 10 1.111 1.58547e-05 12 1.08 5.80613e-06 14 0.959997 0 18 0.957198 2.92453e-05 31 104.52 0.00239929 100 260.35619 -5387.2298 -6434.6688 1047.439 -6534.1958 20.24674 0.07504876 colvars: Saving collective variables state to "peptide2.colvars.state". Loop time of 0.650999 on 4 procs for 100 steps with 2004 atoms Pair time (%) = 0.466917 (71.7232) Bond time (%) = 0.00176847 (0.271655) Kspace time (%) = 0.0588512 (9.04015) Neigh time (%) = 0.0832494 (12.788) Comm time (%) = 0.0190871 (2.93197) Output time (%) = 0.000295341 (0.0453674) Modify time (%) = 0.0194815 (2.99255) Other time (%) = 0.00134867 (0.20717) FFT time (% of Kspce) = 0.010457 (17.7686) FFT Gflps 3d (1d only) = 5.24412 9.93123 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 181777 max 174301 min Histogram: 2 0 0 0 1 0 0 0 0 1 Total # of neighbors = 708233 Ave neighs/atom = 353.41 Ave special neighs/atom = 2.34032 Neighbor list builds = 13 Dangerous builds = 1