164 lines
5.5 KiB
Groff
164 lines
5.5 KiB
Groff
LAMMPS (4 Feb 2020)
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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 1 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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special bonds CPU = 0.000809431 secs
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read_data CPU = 0.0102327 secs
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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 2 all plumed plumedfile plumed.dat outfile p.log
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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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find clusters CPU = 0.000631809 secs
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#dump 1 colvar custom 1 dump.colvar.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_2
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thermo 10
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variable step equal step
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variable pe equal pe
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run 101
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
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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 FFTW3
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3d grid and FFT values/proc = 10648 3375
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmm/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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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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Per MPI rank memory allocation (min/avg/max) = 19.07 | 19.07 | 19.07 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond f_2
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0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
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10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
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20 279.08532 -5226.4036 -6349.1917 1122.7881 -6441.0169 20.764378 0.52605302
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30 282.32141 -5222.3866 -6358.1939 1135.8073 -6448.9785 22.945165 0.65106011
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40 276.34173 -5218.7623 -6330.5128 1111.7504 -6423.7566 15.655345 0.23795099
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50 286.12741 -5215.9248 -6367.0439 1151.1192 -6449.2655 17.420975 0.42646205
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60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815
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70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896
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80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348
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90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 2.06868e-06
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6 0.996999 2.09521e-06
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8 1.08 1.10835e-06
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10 1.111 2.46599e-06
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12 1.08 8.86314e-07
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14 0.959999 0
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18 0.9572 9.14098e-06
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31 104.52 0.000760401
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100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
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101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
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Loop time of 2.69839 on 1 procs for 101 steps with 2004 atoms
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Performance: 6.468 ns/day, 3.711 hours/ns, 37.430 timesteps/s
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99.7% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.2853 | 2.2853 | 2.2853 | 0.0 | 84.69
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Bond | 0.0065637 | 0.0065637 | 0.0065637 | 0.0 | 0.24
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Kspace | 0.14949 | 0.14949 | 0.14949 | 0.0 | 5.54
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Neigh | 0.1938 | 0.1938 | 0.1938 | 0.0 | 7.18
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Comm | 0.0096588 | 0.0096588 | 0.0096588 | 0.0 | 0.36
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Output | 0.00039172 | 0.00039172 | 0.00039172 | 0.0 | 0.01
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Modify | 0.050643 | 0.050643 | 0.050643 | 0.0 | 1.88
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Other | | 0.00258 | | | 0.10
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Nlocal: 2004 ave 2004 max 2004 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11134 ave 11134 max 11134 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 707961 ave 707961 max 707961 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 707961
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Ave neighs/atom = 353.274
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 8
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Dangerous builds = 0
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Total wall time: 0:00:02
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