LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  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
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  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      -6372.3765      1134.9186     -6442.7679      16.557152      273.74323    
        10   333.47919     -4982.3966     -6324.0167      1341.6201     -6400.422       21.367762      12.393263    
        20   309.56902     -4999.498      -6244.9251      1245.4271     -6401.6983      43.59542       13.004313    
        30   316.9763      -5025.5662     -6300.7936      1275.2273     -6422.5376      27.323196      6.7589588    
        40   297.55779     -5088.2203     -6285.325       1197.1047     -6395.3749      13.6769        25.625023    
        50   296.79994     -5117.2966     -6311.3524      1194.0558     -6451.8308      30.631241      5.3320864    
        60   281.72778     -5188.4971     -6321.9161      1133.419      -6427.8858      26.287725      20.574037    
        70   277.26052     -5224.8434     -6340.2902      1115.4468     -6447.8521      27.742891      0.6942037    
        80   268.01485     -5281.8507     -6360.1013      1078.2505     -6496.6085      20.300755      5.2607208    
        90   270.43474     -5334.0836     -6422.0696      1087.986      -6563.2513      39.846097      1.1832275    
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.11096   0.000191462        9
Bond:    6   0.996989  3.55509e-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      1047.4396     -6534.1956      20.246866      0.075048501  
Loop time of 0.25103 on 4 procs for 100 steps with 2004 atoms

Performance: 68.836 ns/day, 0.349 hours/ns, 398.358 timesteps/s, 798.310 katom-step/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    | 0.17407    | 0.17972    | 0.18807    |   1.3 | 71.59
Bond    | 0.00018572 | 0.00048051 | 0.00080203 |   0.0 |  0.19
Kspace  | 0.015736   | 0.023393   | 0.029141   |   3.5 |  9.32
Neigh   | 0.034504   | 0.034509   | 0.03452    |   0.0 | 13.75
Comm    | 0.0063463  | 0.0067336  | 0.0068955  |   0.3 |  2.68
Output  | 0.00011828 | 0.00013486 | 0.00018267 |   0.0 |  0.05
Modify  | 0.0055927  | 0.0056488  | 0.0057029  |   0.1 |  2.25
Other   |            | 0.0004124  |            |       |  0.16

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
