forked from lijiext/lammps
151 lines
4.8 KiB
Plaintext
151 lines
4.8 KiB
Plaintext
LAMMPS (20 Mar 2014-ICMS)
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WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
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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 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
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fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
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fix 2a ref setforce 0.0 0.0 0.0
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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.spring.lammpstrj id xu yu zu fx fy fz
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dump_modify 1 sort id
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variable sp equal f_3a+f_3b
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thermo_style custom step temp etotal pe ke epair ebond v_sp
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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 = 11.5952 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond sp
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0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
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10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344
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20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706
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30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914
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40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396
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50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459511 0.20679816
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60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527
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70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.627151 11.433633
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80 267.51476 -5206.4042 -6282.6428 1076.2386 -6456.6353 31.611841 6.3553235
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90 278.15512 -5245.383 -6364.4289 1119.0458 -6499.8037 28.849902 0.36938816
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SHAKE stats (type/ave/delta) on step 100
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4 1.11098 8.97185e-05
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6 0.996996 1.00569e-05
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8 1.08 6.02346e-06
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10 1.111 1.84257e-05
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12 1.08 7.27136e-06
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14 0.959996 0
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18 0.957198 3.36078e-05
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31 104.52 0.00306008
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100 260.10505 -5292.689 -6339.1176 1046.4286 -6471.6693 25.361881 0.21986866
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Loop time of 1.07153 on 2 procs for 100 steps with 2004 atoms
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98.1% CPU use with 2 MPI tasks x 1 OpenMP threads
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Performance: 16.126 ns/day 1.488 hours/ns 93.325 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 | 0.76688 | 0.77633 | 0.78579 | 1.1 | 72.45
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Bond | 0.0024021 | 0.0025222 | 0.0026424 | 0.2 | 0.24
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Kspace | 0.095468 | 0.10394 | 0.1124 | 2.6 | 9.70
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Neigh | 0.13518 | 0.13518 | 0.13519 | 0.0 | 12.62
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Comm | 0.018154 | 0.018954 | 0.019754 | 0.6 | 1.77
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Output | 0.005975 | 0.0066451 | 0.0073152 | 0.8 | 0.62
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Modify | 0.025297 | 0.025306 | 0.025314 | 0.0 | 2.36
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Other | | 0.002651 | | | 0.25
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Nlocal: 1002 ave 1013 max 991 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8629.5 ave 8641 max 8618 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 354118 ave 356534 max 351703 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 708237
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Ave neighs/atom = 353.412
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 12
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Dangerous builds = 2
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