Homec4science
Diffusion lammps (master) Browse

lammps/examples/USER/cg-cmm/peg-verlet/log.pegc12e8
5683091bfb4cmaster

Last Change
Raw File

log.pegc12e8
View Options

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
# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
bond_style harmonic
angle_style harmonic
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
angle_coeff 2 3.400 132.0
angle_coeff 3 3.200 146.0
angle_coeff 4 1.500 172.0
angle_coeff 5 1.190 173.0
angle_coeff 6 1.600 172.0
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 = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
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 = 27.1134 (sec) ----------------
TotEng = -217991.2189 KinEng = 36188.3877 Temp = 302.4603
PotEng = -254179.6067 E_bond = 4590.3067 E_angle = 3421.2609
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262191.1742
E_coul = 0.0000 E_long = 0.0000 Press = 37.0652
---------------- Step 400 ----- CPU = 55.8229 (sec) ----------------
TotEng = -217934.5954 KinEng = 36330.2463 Temp = 303.6459
PotEng = -254264.8418 E_bond = 4626.8916 E_angle = 3512.1639
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262403.8973
E_coul = 0.0000 E_long = 0.0000 Press = 17.4311
---------------- Step 600 ----- CPU = 83.0111 (sec) ----------------
TotEng = -218281.8191 KinEng = 36141.0168 Temp = 302.0644
PotEng = -254422.8358 E_bond = 4628.2093 E_angle = 3492.7509
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262543.7960
E_coul = 0.0000 E_long = 0.0000 Press = 9.5773
---------------- Step 800 ----- CPU = 110.5361 (sec) ----------------
TotEng = -218232.9755 KinEng = 36343.0623 Temp = 303.7531
PotEng = -254576.0378 E_bond = 4659.4462 E_angle = 3567.9426
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262803.4265
E_coul = 0.0000 E_long = 0.0000 Press = -9.6008
---------------- Step 1000 ----- CPU = 137.3658 (sec) ----------------
TotEng = -218073.8055 KinEng = 36426.1635 Temp = 304.4476
PotEng = -254499.9689 E_bond = 4602.2406 E_angle = 3636.2557
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262738.4653
E_coul = 0.0000 E_long = 0.0000 Press = -11.9067
Loop time of 137.366 on 4 procs for 1000 steps with 40140 atoms
Performance: 3.145 ns/day 7.631 hours/ns
Pair time (%) = 59.0174 (42.9636)
Bond time (%) = 0.932444 (0.678802)
Neigh time (%) = 6.30874 (4.59265)
Comm time (%) = 69.5999 (50.6674)
Outpt time (%) = 0.0389841 (0.0283797)
Other time (%) = 1.46867 (1.06916)
Nlocal: 10035 ave 19552 max 532 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 11779.5 ave 18122 max 5457 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.19488e+06 ave 2.39205e+06 max 12991 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 4779515
Ave neighs/atom = 119.071
Ave special neighs/atom = 1.26861
Neighbor list builds = 61
Dangerous builds = 0
write_restart pegc12e8-1.restart
c4science · Help