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lammps/examples/USER/colvars/log.peptide-spring
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LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
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 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 ...
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 = 6776 1800
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 = 11.5952 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond sp
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344
20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706
30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914
40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396
50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459511 0.20679816
60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527
70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.627151 11.433633
80 267.51476 -5206.4042 -6282.6428 1076.2386 -6456.6353 31.611841 6.3553235
90 278.15512 -5245.383 -6364.4289 1119.0458 -6499.8037 28.849902 0.36938816
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97185e-05
6 0.996996 1.00569e-05
8 1.08 6.02346e-06
10 1.111 1.84257e-05
12 1.08 7.27136e-06
14 0.959996 0
18 0.957198 3.36078e-05
31 104.52 0.00306008
100 260.10505 -5292.689 -6339.1176 1046.4286 -6471.6693 25.361881 0.21986866
Loop time of 1.07153 on 2 procs for 100 steps with 2004 atoms
98.1% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 16.126 ns/day 1.488 hours/ns 93.325 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.76688 | 0.77633 | 0.78579 | 1.1 | 72.45
Bond | 0.0024021 | 0.0025222 | 0.0026424 | 0.2 | 0.24
Kspace | 0.095468 | 0.10394 | 0.1124 | 2.6 | 9.70
Neigh | 0.13518 | 0.13518 | 0.13519 | 0.0 | 12.62
Comm | 0.018154 | 0.018954 | 0.019754 | 0.6 | 1.77
Output | 0.005975 | 0.0066451 | 0.0073152 | 0.8 | 0.62
Modify | 0.025297 | 0.025306 | 0.025314 | 0.0 | 2.36
Other | | 0.002651 | | | 0.25
Nlocal: 1002 ave 1013 max 991 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8629.5 ave 8641 max 8618 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354118 ave 356534 max 351703 min
Histogram: 1 0 0 0 0 0 0 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
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