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
