147 lines
5.5 KiB
Plaintext
147 lines
5.5 KiB
Plaintext
LAMMPS (21 Dec 2011-ICMS)
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using 1 OpenMP thread(s) per MPI task
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# Solvated 5-mer peptide
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units real
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dimension 3
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atom_style angle
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# enforce that in z-direction there is only one
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# processor (could be two) for optimal performance
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processors * * 1
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# read topology and force field
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read_data data.pegc12e8
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1 = max bonds/atom
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1 = max angles/atom
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orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
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4 by 2 by 1 MPI processor grid
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40140 atoms
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13284 bonds
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12177 angles
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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include parm.pegc12e8
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# Solvated 5-mer peptide CG force field
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pair_style lj/sdk 15.0
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bond_style harmonic
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angle_style harmonic
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special_bonds lj/coul 0.0 0.0 1.0
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of special neighbors
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mass 1 31.035
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mass 2 44.054
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mass 3 42.081
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mass 4 29.062
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mass 5 54.000
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pair_coeff 1 1 lj9_6 0.4491 3.7130
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pair_coeff 1 2 lj9_6 0.4400 3.8900
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pair_coeff 1 3 lj9_6 0.3650 3.9870
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pair_coeff 1 4 lj9_6 0.3800 3.8400
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pair_coeff 1 5 lj12_4 0.7000 3.9500
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pair_coeff 2 2 lj9_6 0.4050 4.2500
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pair_coeff 2 3 lj9_6 0.3770 4.2740
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pair_coeff 2 4 lj9_6 0.3700 4.1400
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pair_coeff 2 5 lj12_4 0.5700 4.3100
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pair_coeff 3 3 lj9_6 0.4200 4.5060
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pair_coeff 3 4 lj9_6 0.3620 4.3635
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pair_coeff 3 5 lj12_4 0.3400 4.4385
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pair_coeff 4 4 lj9_6 0.3120 4.2210
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pair_coeff 4 5 lj12_4 0.2900 4.2960
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pair_coeff 5 5 lj12_4 0.8950 4.3710
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bond_coeff 1 15.00 2.79
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bond_coeff 2 4.900 3.28
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bond_coeff 3 7.100 3.56
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bond_coeff 4 6.160 3.64
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bond_coeff 5 9.000 3.13
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angle_coeff 1 3.000 131.0
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angle_coeff 2 3.400 132.0
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angle_coeff 3 3.200 146.0
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angle_coeff 4 1.500 172.0
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angle_coeff 5 1.190 173.0
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angle_coeff 6 1.600 172.0
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neighbor 3.0 bin
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neigh_modify delay 5
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timestep 5.0
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#dump 1 all xtc 200 pegc12e8-1.xtc
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#dump_modify 1 unwrap yes
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#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
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#dump_modify 2 unwrap yes
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velocity all create 303.0 46659 mom yes rot yes dist gaussian
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fix 1 all nvt temp 303.0 303.0 100.0
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thermo_style multi
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thermo 200
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run 1000
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Memory usage per processor = 10.0915 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
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PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
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E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
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---------------- Step 200 ----- CPU = 2.8323 (sec) ----------------
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TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
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PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
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E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
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---------------- Step 400 ----- CPU = 5.8481 (sec) ----------------
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TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
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PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
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E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
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---------------- Step 600 ----- CPU = 8.8857 (sec) ----------------
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TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
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PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
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E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
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---------------- Step 800 ----- CPU = 11.9061 (sec) ----------------
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TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
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PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
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E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
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---------------- Step 1000 ----- CPU = 14.9738 (sec) ----------------
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TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
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PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
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E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
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Loop time of 14.9738 on 8 procs (8 MPI x 1 OpenMP) for 1000 steps with 40140 atoms
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Performance: 28.850 ns/day 0.832 hours/ns 66.783 timesteps/s
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Section | min time | avg time | max time |%total | #Thr
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--------------------------------------------------------------
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Pair | 11.92 | 12.15 | 12.39 | 81.13 | 1.0x
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Bond | 0.2939 | 0.3141 | 0.3283 | 2.10 | 1.0x
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Neigh | 1.068 | 1.09 | 1.119 | 7.28 | 1.0x
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Comm | 0.8103 | 1.091 | 1.341 | 7.29 | 1.0x
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Output | 0.0003598 | 0.0003798 | 0.0005069 | 0.00 | 1.0x
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Modify | 0.1976 | 0.2041 | 0.2086 | 1.36 | 0.9x
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Other | | 0.1261 | | 0.84 |
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Nlocal: 5017.5 ave 5051 max 4982 min
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Histogram: 1 2 0 0 1 0 1 1 0 2
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Nghost: 11697.4 ave 11771 max 11645 min
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Histogram: 3 0 0 0 2 1 0 1 0 1
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Neighs: 711460 ave 720454 max 704238 min
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Histogram: 2 1 1 0 0 1 1 1 0 1
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Total # of neighbors = 5691680
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Ave neighs/atom = 141.796
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Ave special neighs/atom = 1.26861
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Neighbor list builds = 38
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Dangerous builds = 0
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#write_restart pegc12e8-1.restart
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