146 lines
4.7 KiB
Plaintext
146 lines
4.7 KiB
Plaintext
LAMMPS (5 Nov 2014-ICMS)
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WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:88)
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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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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 1 by 2 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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2004 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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14 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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1365 bonds
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reading angles ...
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786 angles
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reading dihedrals ...
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207 dihedrals
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reading impropers ...
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12 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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group peptide type <= 12
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84 atoms in group peptide
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group one id 2 4 5 6
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4 atoms in group one
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group two id 80 82 83 84
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4 atoms in group two
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group ref id 37
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1 atoms in group ref
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group colvar union one two ref
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9 atoms in group colvar
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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thermo_style custom step temp etotal pe ke epair ebond f_3
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thermo 10
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run 100
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PPPM initialization ...
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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 6776 1800
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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Memory usage per processor = 14.8025 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond 3
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0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
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10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
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20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393
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30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
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40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
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50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
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60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8834 26.28765 20.573958
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70 277.26045 -5224.8415 -6340.288 1115.4465 -6447.8494 27.742889 0.69414895
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80 268.01458 -5281.8501 -6360.0995 1078.2495 -6496.6062 20.300729 5.260642
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90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
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SHAKE stats (type/ave/delta) on step 100
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4 1.11096 0.000191466
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6 0.996989 3.5552e-05
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8 1.08 9.10001e-06
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10 1.111 1.58547e-05
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12 1.08 5.80613e-06
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14 0.959997 0
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18 0.957198 2.92454e-05
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31 104.52 0.00239929
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100 260.35617 -5387.2297 -6434.6686 1047.4389 -6534.1956 20.246734 0.075048996
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Loop time of 1.08261 on 2 procs for 100 steps with 2004 atoms
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99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
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Performance: 15.961 ns/day 1.504 hours/ns 92.369 timesteps/s
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MPI task timings breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.78993 | 0.79433 | 0.79873 | 0.5 | 73.37
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Bond | 0.0024209 | 0.0026361 | 0.0028512 | 0.4 | 0.24
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Kspace | 0.088027 | 0.092698 | 0.097369 | 1.5 | 8.56
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Neigh | 0.15101 | 0.15101 | 0.15102 | 0.0 | 13.95
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Comm | 0.01659 | 0.017051 | 0.017513 | 0.4 | 1.58
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Output | 0.00024629 | 0.00033844 | 0.00043058 | 0.5 | 0.03
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Modify | 0.022275 | 0.02228 | 0.022284 | 0.0 | 2.06
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Other | | 0.002267 | | | 0.21
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Nlocal: 1002 ave 1010 max 994 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8645 ave 8652 max 8638 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 354116 ave 356373 max 351860 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 708233
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Ave neighs/atom = 353.41
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 13
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Dangerous builds = 1
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