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lammps/examples/USER/cg-cmm/peg-verlet/log.pegc12e8-angle
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LAMMPS (21 Dec 2011-ICMS)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# enforce that in z-direction there is only one
# processor (could be two) for optimal performance
processors * * 1
# 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)
4 by 2 by 1 MPI 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 lj/sdk 15.0
bond_style harmonic
angle_style sdk
special_bonds lj/coul 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 temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 9.68794 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 = 114.4952
---------------- Step 200 ----- CPU = 2.7456 (sec) ----------------
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
---------------- Step 400 ----- CPU = 5.5655 (sec) ----------------
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
---------------- Step 600 ----- CPU = 8.3509 (sec) ----------------
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
---------------- Step 800 ----- CPU = 11.2052 (sec) ----------------
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
---------------- Step 1000 ----- CPU = 14.0956 (sec) ----------------
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
Loop time of 14.0956 on 8 procs (8 MPI x 1 OpenMP) for 1000 steps with 40140 atoms
Performance: 30.648 ns/day 0.783 hours/ns 70.944 timesteps/s
Section | min time | avg time | max time |%total | #Thr
--------------------------------------------------------------
Pair | 10.92 | 11.06 | 11.22 | 78.46 | 1.0x
Bond | 0.3011 | 0.3112 | 0.3199 | 2.21 | 1.0x
Neigh | 1.522 | 1.543 | 1.567 | 10.94 | 1.0x
Comm | 0.696 | 0.8695 | 1.044 | 6.17 | 1.0x
Output | 0.0003402 | 0.000362 | 0.0004911 | 0.00 | 1.0x
Modify | 0.1941 | 0.2011 | 0.2144 | 1.43 | 1.0x
Other | | 0.1113 | | 0.79 |
Nlocal: 5017.5 ave 5041 max 4963 min
Histogram: 1 0 0 0 0 2 1 0 1 3
Nghost: 10895.1 ave 10955 max 10838 min
Histogram: 2 1 0 1 0 0 0 2 1 1
Neighs: 596997 ave 602732 max 590121 min
Histogram: 1 0 1 0 1 1 1 1 1 1
Total # of neighbors = 4775973
Ave neighs/atom = 118.983
Ave special neighs/atom = 1.26861
Neighbor list builds = 59
Dangerous builds = 0
#write_restart pegc12e8-angle-1.restart
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