139 lines
5.0 KiB
Plaintext
139 lines
5.0 KiB
Plaintext
LAMMPS (22 Jan 2008 / Patchlevel 25 Jan 2008 / CMM-CG v0.97)
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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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# 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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1 by 1 by 4 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 cg/cmm 15.0
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bond_style harmonic
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angle_style harmonic
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special_bonds 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 2.0 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 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 = 4.43925 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 = 27.1134 (sec) ----------------
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TotEng = -217991.2189 KinEng = 36188.3877 Temp = 302.4603
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PotEng = -254179.6067 E_bond = 4590.3067 E_angle = 3421.2609
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262191.1742
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E_coul = 0.0000 E_long = 0.0000 Press = 37.0652
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---------------- Step 400 ----- CPU = 55.8229 (sec) ----------------
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TotEng = -217934.5954 KinEng = 36330.2463 Temp = 303.6459
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PotEng = -254264.8418 E_bond = 4626.8916 E_angle = 3512.1639
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262403.8973
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E_coul = 0.0000 E_long = 0.0000 Press = 17.4311
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---------------- Step 600 ----- CPU = 83.0111 (sec) ----------------
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TotEng = -218281.8191 KinEng = 36141.0168 Temp = 302.0644
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PotEng = -254422.8358 E_bond = 4628.2093 E_angle = 3492.7509
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262543.7960
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E_coul = 0.0000 E_long = 0.0000 Press = 9.5773
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---------------- Step 800 ----- CPU = 110.5361 (sec) ----------------
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TotEng = -218232.9755 KinEng = 36343.0623 Temp = 303.7531
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PotEng = -254576.0378 E_bond = 4659.4462 E_angle = 3567.9426
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262803.4265
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E_coul = 0.0000 E_long = 0.0000 Press = -9.6008
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---------------- Step 1000 ----- CPU = 137.3658 (sec) ----------------
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TotEng = -218073.8055 KinEng = 36426.1635 Temp = 304.4476
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PotEng = -254499.9689 E_bond = 4602.2406 E_angle = 3636.2557
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262738.4653
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E_coul = 0.0000 E_long = 0.0000 Press = -11.9067
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Loop time of 137.366 on 4 procs for 1000 steps with 40140 atoms
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Performance: 3.145 ns/day 7.631 hours/ns
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Pair time (%) = 59.0174 (42.9636)
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Bond time (%) = 0.932444 (0.678802)
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Neigh time (%) = 6.30874 (4.59265)
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Comm time (%) = 69.5999 (50.6674)
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Outpt time (%) = 0.0389841 (0.0283797)
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Other time (%) = 1.46867 (1.06916)
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Nlocal: 10035 ave 19552 max 532 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 11779.5 ave 18122 max 5457 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 1.19488e+06 ave 2.39205e+06 max 12991 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 4779515
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Ave neighs/atom = 119.071
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Ave special neighs/atom = 1.26861
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Neighbor list builds = 61
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Dangerous builds = 0
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write_restart pegc12e8-1.restart
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