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lammps/examples/peptide/log.5Oct16.peptide.g++.4
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LAMMPS (5 Oct 2016)
# 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 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
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
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
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
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 ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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 = 4312 960
Neighbor list info ...
1 neighbor list requests
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
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 = 14.8928 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112
---------------- Step 50 ----- CPU = 0.2741 (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 = -1331.7946
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80613e-07
6 0.997 1.06181e-06
8 1.08 6.20292e-07
10 1.111 6.23284e-07
12 1.08 2.67996e-07
14 0.96 0
18 0.957201 5.3796e-06
31 104.52 0.000502278
---------------- Step 100 ----- CPU = 0.5371 (sec) ----------------
TotEng = -5257.9979 KinEng = 1078.0553 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 = -648.6819
---------------- Step 150 ----- CPU = 0.8054 (sec) ----------------
TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737
PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594
E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675
E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1830
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18699e-07
6 0.997 1.50563e-07
8 1.08 6.57501e-08
10 1.111 5.54188e-07
12 1.08 1.98841e-07
14 0.96 0
18 0.957201 3.59627e-06
31 104.52 0.000388336
---------------- Step 200 ----- CPU = 1.0652 (sec) ----------------
TotEng = -5308.4465 KinEng = 1100.4875 Temp = 273.5422
PotEng = -6408.9340 E_bond = 18.2714 E_angle = 33.3040
E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221
E_coul = 26736.1321 E_long = -33902.3837 Press = -1470.3400
---------------- Step 250 ----- CPU = 1.3409 (sec) ----------------
TotEng = -5294.1570 KinEng = 1071.0939 Temp = 266.2360
PotEng = -6365.2509 E_bond = 14.2013 E_angle = 39.1996
E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4591
E_coul = 26714.0037 E_long = -33908.7139 Press = -189.6059
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.79043e-06
6 0.997001 3.60519e-06
8 1.08 2.09368e-06
10 1.111 5.64839e-06
12 1.08 2.10676e-06
14 0.96 0
18 0.957202 7.72573e-06
31 104.52 0.000806208
---------------- Step 300 ----- CPU = 1.6199 (sec) ----------------
TotEng = -5251.3639 KinEng = 1123.7721 Temp = 279.3299
PotEng = -6375.1360 E_bond = 14.2206 E_angle = 38.4274
E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3470
E_coul = 26745.4071 E_long = -33909.0790 Press = -471.5569
Loop time of 1.61992 on 4 procs for 300 steps with 2004 atoms
Performance: 32.002 ns/day, 0.750 hours/ns, 185.194 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1484 | 1.17 | 1.1865 | 1.5 | 72.23
Bond | 0.0011752 | 0.003831 | 0.0069602 | 4.0 | 0.24
Kspace | 0.16316 | 0.1798 | 0.20413 | 3.9 | 11.10
Neigh | 0.16885 | 0.16895 | 0.16902 | 0.0 | 10.43
Comm | 0.046479 | 0.047215 | 0.047759 | 0.2 | 2.91
Output | 0.00024033 | 0.00025702 | 0.00030375 | 0.2 | 0.02
Modify | 0.04556 | 0.045949 | 0.046353 | 0.2 | 2.84
Other | | 0.003923 | | | 0.24
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6587.75 ave 6632 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177005 ave 180556 max 170207 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 708020
Ave neighs/atom = 353.303
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
Total wall time: 0:00:01
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