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 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

thermo_style    multi
thermo          50

fix             1 all nvt temp 275.0 275.0 100.0 tchain 1
fix             2 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

group           peptide type <= 12
84 atoms in group peptide

#dump           1 peptide atom 10 dump.peptide

#dump           2 peptide image 25 image.*.jpg type type #               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify    2 pad 3

#dump           3 peptide movie 25 movie.mpg type type #               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify    3 pad 3

#compute                bnd all property/local btype batom1 batom2
#dump           2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]

run             300
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 = 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              0 ----- CPU =            0 (sec) -------------
TotEng   =     -5237.4580 KinEng   =      1134.9186 Temp     =       282.1005 
PotEng   =     -6372.3765 E_bond   =        16.5572 E_angle  =        36.3726 
E_dihed  =        15.5190 E_impro  =         1.9426 E_vdwl   =       692.8945 
E_coul   =     26772.2647 E_long   =    -33907.9271 Press    =      -837.0111
------------ Step             50 ----- CPU =     0.402928 (sec) -------------
TotEng   =     -5247.5537 KinEng   =      1132.4000 Temp     =       281.4745 
PotEng   =     -6379.9537 E_bond   =        12.2118 E_angle  =        31.7365 
E_dihed  =        18.8145 E_impro  =         2.3611 E_vdwl   =       658.1785 
E_coul   =     26804.4441 E_long   =    -33907.7003 Press    =     -1331.7945
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.111     7.80612e-07        9
Bond:    6   0.997     1.0618e-06         6
Bond:    8   1.08      6.20292e-07        7
Bond:   10   1.111     6.23283e-07        8
Bond:   12   1.08      2.67996e-07        9
Bond:   14   0.96      0                  1
Bond:   18   0.957201  5.3796e-06      1280
Angle:  31   104.52    0.000502278      640
------------ Step            100 ----- CPU =    0.8040338 (sec) -------------
TotEng   =     -5257.9979 KinEng   =      1078.0552 Temp     =       267.9663 
PotEng   =     -6336.0532 E_bond   =        14.4829 E_angle  =        43.4429 
E_dihed  =        15.2569 E_impro  =         2.3160 E_vdwl   =       708.3273 
E_coul   =     26786.6829 E_long   =    -33906.5621 Press    =      -648.6817
------------ Step            150 ----- CPU =     1.222416 (sec) -------------
TotEng   =     -5287.2798 KinEng   =      1098.6027 Temp     =       273.0737 
PotEng   =     -6385.8825 E_bond   =        17.4925 E_angle  =        32.8594 
E_dihed  =        15.1624 E_impro  =         1.6522 E_vdwl   =       736.9676 
E_coul   =     26717.2655 E_long   =    -33907.2820 Press    =      -333.1814
SHAKE stats (type/ave/delta/count) on step 200
Bond:    4   1.111     2.18704e-07        9
Bond:    6   0.997     1.50575e-07        6
Bond:    8   1.08      6.57544e-08        7
Bond:   10   1.111     5.54343e-07        8
Bond:   12   1.08      1.98861e-07        9
Bond:   14   0.96      0                  1
Bond:   18   0.957201  3.59631e-06     1280
Angle:  31   104.52    0.000388324      640
------------ Step            200 ----- CPU =     1.620976 (sec) -------------
TotEng   =     -5308.4469 KinEng   =      1100.4878 Temp     =       273.5422 
PotEng   =     -6408.9346 E_bond   =        18.2714 E_angle  =        33.3040 
E_dihed  =        16.8151 E_impro  =         2.6051 E_vdwl   =       686.3219 
E_coul   =     26736.1320 E_long   =    -33902.3841 Press    =     -1470.3472
------------ Step            250 ----- CPU =     2.042726 (sec) -------------
TotEng   =     -5294.1562 KinEng   =      1071.0934 Temp     =       266.2358 
PotEng   =     -6365.2496 E_bond   =        14.2013 E_angle  =        39.1995 
E_dihed  =        19.4583 E_impro  =         3.1406 E_vdwl   =       753.4711 
E_coul   =     26713.9935 E_long   =    -33908.7140 Press    =      -189.4392
SHAKE stats (type/ave/delta/count) on step 300
Bond:    4   1.111     3.7902e-06         9
Bond:    6   0.997001  3.60123e-06        6
Bond:    8   1.08      2.09366e-06        7
Bond:   10   1.111     5.64813e-06        8
Bond:   12   1.08      2.10662e-06        9
Bond:   14   0.96      0                  1
Bond:   18   0.957202  7.7167e-06      1280
Angle:  31   104.52    0.000806198      640
------------ Step            300 ----- CPU =     2.466484 (sec) -------------
TotEng   =     -5251.3634 KinEng   =      1123.7660 Temp     =       279.3284 
PotEng   =     -6375.1294 E_bond   =        14.2208 E_angle  =        38.4294 
E_dihed  =        18.1660 E_impro  =         2.3732 E_vdwl   =       715.3636 
E_coul   =     26745.3993 E_long   =    -33909.0817 Press    =      -471.3012
Loop time of 2.4665 on 1 procs for 300 steps with 2004 atoms

Performance: 21.018 ns/day, 1.142 hours/ns, 121.630 timesteps/s, 243.746 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    | 2.0358     | 2.0358     | 2.0358     |   0.0 | 82.54
Bond    | 0.0038336  | 0.0038336  | 0.0038336  |   0.0 |  0.16
Kspace  | 0.12307    | 0.12307    | 0.12307    |   0.0 |  4.99
Neigh   | 0.26577    | 0.26577    | 0.26577    |   0.0 | 10.78
Comm    | 0.0090043  | 0.0090043  | 0.0090043  |   0.0 |  0.37
Output  | 0.00018762 | 0.00018762 | 0.00018762 |   0.0 |  0.01
Modify  | 0.02741    | 0.02741    | 0.02741    |   0.0 |  1.11
Other   |            | 0.001442   |            |       |  0.06

Nlocal:           2004 ave        2004 max        2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          11185 ave       11185 max       11185 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         708024 ave      708024 max      708024 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708024
Ave neighs/atom = 353.30539
Ave special neighs/atom = 2.3403194
Neighbor list builds = 26
Dangerous builds = 0

Total wall time: 0:00:02
