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lammps/examples/peptide/log.5Oct16.peptide.g++.1
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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 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
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 = 10648 3375
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 = 15.5934 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 = 0.9457 (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 = 1.9163 (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 = 2.9286 (sec) ----------------
TotEng = -5287.2798 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 = -333.1829
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18698e-07
6 0.997 1.50562e-07
8 1.08 6.57498e-08
10 1.111 5.54188e-07
12 1.08 1.98839e-07
14 0.96 0
18 0.957201 3.59627e-06
31 104.52 0.000388335
---------------- Step 200 ----- CPU = 3.8703 (sec) ----------------
TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421
PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040
E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221
E_coul = 26736.1319 E_long = -33902.3837 Press = -1470.3400
---------------- Step 250 ----- CPU = 4.8652 (sec) ----------------
TotEng = -5294.1569 KinEng = 1071.0938 Temp = 266.2359
PotEng = -6365.2507 E_bond = 14.2013 E_angle = 39.1996
E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4590
E_coul = 26714.0040 E_long = -33908.7139 Press = -189.6059
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.79044e-06
6 0.997001 3.6052e-06
8 1.08 2.09369e-06
10 1.111 5.6484e-06
12 1.08 2.10677e-06
14 0.96 0
18 0.957202 7.72576e-06
31 104.52 0.000806204
---------------- Step 300 ----- CPU = 5.8596 (sec) ----------------
TotEng = -5251.3637 KinEng = 1123.7718 Temp = 279.3298
PotEng = -6375.1355 E_bond = 14.2206 E_angle = 38.4274
E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3473
E_coul = 26745.4074 E_long = -33909.0791 Press = -471.5505
Loop time of 5.85959 on 1 procs for 300 steps with 2004 atoms
Performance: 8.847 ns/day, 2.713 hours/ns, 51.198 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.6289 | 4.6289 | 4.6289 | 0.0 | 79.00
Bond | 0.013405 | 0.013405 | 0.013405 | 0.0 | 0.23
Kspace | 0.47821 | 0.47821 | 0.47821 | 0.0 | 8.16
Neigh | 0.64447 | 0.64447 | 0.64447 | 0.0 | 11.00
Comm | 0.026137 | 0.026137 | 0.026137 | 0.0 | 0.45
Output | 0.00018501 | 0.00018501 | 0.00018501 | 0.0 | 0.00
Modify | 0.062095 | 0.062095 | 0.062095 | 0.0 | 1.06
Other | | 0.006195 | | | 0.11
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: 708018 ave 708018 max 708018 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708018
Ave neighs/atom = 353.302
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
Total wall time: 0:00:05
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