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lammps/examples/USER/cg-cmm/peg-verlet/log.pegc12e8-angle
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LAMMPS (22 Jan 2008 / Patchlevel 25 Jan 2008 / CMM-CG v0.97)
# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# read topology and force field
read_data data.pegc12e8
1 = max bonds/atom
1 = max angles/atom
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
1 by 1 by 4 processor grid
40140 atoms
13284 bonds
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
include parm.pegc12e8-angle
# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
bond_style harmonic
angle_style cg/cmm
special_bonds 0.0 0.0 1.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
mass 1 31.035
mass 2 44.054
mass 3 42.081
mass 4 29.062
mass 5 54.000
pair_coeff 1 1 lj9_6 0.4491 3.7130
pair_coeff 1 2 lj9_6 0.4400 3.8900
pair_coeff 1 3 lj9_6 0.3650 3.9870
pair_coeff 1 4 lj9_6 0.3800 3.8400
pair_coeff 1 5 lj12_4 0.7000 3.9500
pair_coeff 2 2 lj9_6 0.4050 4.2500
pair_coeff 2 3 lj9_6 0.3770 4.2740
pair_coeff 2 4 lj9_6 0.3700 4.1400
pair_coeff 2 5 lj12_4 0.5700 4.3100
pair_coeff 3 3 lj9_6 0.4200 4.5060
pair_coeff 3 4 lj9_6 0.3620 4.3635
pair_coeff 3 5 lj12_4 0.3400 4.4385
pair_coeff 4 4 lj9_6 0.3120 4.2210
pair_coeff 4 5 lj12_4 0.2900 4.2960
pair_coeff 5 5 lj12_4 0.8950 4.3710
bond_coeff 1 15.00 2.79
bond_coeff 2 4.900 3.28
bond_coeff 3 7.100 3.56
bond_coeff 4 6.160 3.64
bond_coeff 5 9.000 3.13
angle_coeff 1 3.000 131.0 lj9_6 0.4400 3.8900
angle_coeff 2 3.400 132.0 lj9_6 0.4050 4.2500
angle_coeff 3 3.200 146.0 lj9_6 0.3770 4.2740
angle_coeff 4 1.500 172.0 lj9_6 0.3770 4.2740
angle_coeff 5 1.190 173.0 lj9_6 0.4200 4.5060
angle_coeff 6 1.600 172.0 lj9_6 0.3620 4.3635
neighbor 2.0 bin
neigh_modify delay 5
timestep 5.0
dump 1 all xtc 200 pegc12e8-1.xtc
dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 4.43925 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
---------------- Step 200 ----- CPU = 29.9183 (sec) ----------------
TotEng = -218051.4566 KinEng = 36272.3725 Temp = 303.1622
PotEng = -254323.8292 E_bond = 4530.3699 E_angle = 3351.7084
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.9074
E_coul = 0.0000 E_long = 0.0000 Press = 36.2458
---------------- Step 400 ----- CPU = 60.9372 (sec) ----------------
TotEng = -218054.5847 KinEng = 36253.0519 Temp = 303.0008
PotEng = -254307.6366 E_bond = 4620.3304 E_angle = 3417.4287
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262345.3957
E_coul = 0.0000 E_long = 0.0000 Press = 12.6545
---------------- Step 600 ----- CPU = 89.8983 (sec) ----------------
TotEng = -218042.2111 KinEng = 36394.6544 Temp = 304.1843
PotEng = -254436.8655 E_bond = 4623.6900 E_angle = 3419.7393
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262480.2949
E_coul = 0.0000 E_long = 0.0000 Press = 20.4952
---------------- Step 800 ----- CPU = 119.1245 (sec) ----------------
TotEng = -217865.4500 KinEng = 36565.4671 Temp = 305.6119
PotEng = -254430.9171 E_bond = 4590.5794 E_angle = 3466.0941
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262487.5906
E_coul = 0.0000 E_long = 0.0000 Press = 2.9466
---------------- Step 1000 ----- CPU = 147.8398 (sec) ----------------
TotEng = -218219.2310 KinEng = 36266.8018 Temp = 303.1157
PotEng = -254486.0328 E_bond = 4542.7739 E_angle = 3415.8267
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262444.6334
E_coul = 0.0000 E_long = 0.0000 Press = -8.6110
Loop time of 147.84 on 4 procs for 1000 steps with 40140 atoms
Performance: 2.922 ns/day 8.213 hours/ns
Pair time (%) = 61.7803 (41.7886)
Bond time (%) = 1.17913 (0.797574)
Neigh time (%) = 6.23896 (4.22007)
Comm time (%) = 76.805 (51.9514)
Outpt time (%) = 0.0374529 (0.0253334)
Other time (%) = 1.79919 (1.21699)
Nlocal: 10035 ave 19571 max 538 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 11797.5 ave 18129 max 5484 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.19407e+06 ave 2.388e+06 max 12690 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 4776294
Ave neighs/atom = 118.991
Ave special neighs/atom = 1.26861
Neighbor list builds = 59
Dangerous builds = 0
write_restart pegc12e8-angle-1.restart
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