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lammps/examples/USER/colvars/log.peptide-spring2
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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 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
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.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 ...
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 3
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 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 -6401.6969 43.595447 13.004393
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8834 26.28765 20.573958
70 277.26045 -5224.8415 -6340.288 1115.4465 -6447.8494 27.742889 0.69414895
80 268.01458 -5281.8501 -6360.0995 1078.2495 -6496.6062 20.300729 5.260642
90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
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 2.92454e-05
31 104.52 0.00239929
100 260.35617 -5387.2297 -6434.6686 1047.4389 -6534.1956 20.246734 0.075048996
Loop time of 1.07264 on 2 procs for 100 steps with 2004 atoms
98.6% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 16.110 ns/day 1.490 hours/ns 93.228 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.76647 | 0.77219 | 0.77792 | 0.7 | 71.99
Bond | 0.0024974 | 0.0025403 | 0.0025833 | 0.1 | 0.24
Kspace | 0.091998 | 0.096921 | 0.10184 | 1.6 | 9.04
Neigh | 0.14764 | 0.14765 | 0.14767 | 0.0 | 13.77
Comm | 0.018904 | 0.01937 | 0.019835 | 0.3 | 1.81
Output | 0.005985 | 0.0067209 | 0.0074568 | 0.9 | 0.63
Modify | 0.024529 | 0.024536 | 0.024542 | 0.0 | 2.29
Other | | 0.002705 | | | 0.25
Nlocal: 1002 ave 1010 max 994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8645 ave 8652 max 8638 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354116 ave 356373 max 351860 min
Histogram: 1 0 0 0 0 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
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