mirror of https://github.com/lammps/lammps.git
190 lines
6.9 KiB
Groff
190 lines
6.9 KiB
Groff
LAMMPS (15 Feb 2016)
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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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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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thermo_style multi
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thermo 50
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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fix 2 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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group peptide type <= 12
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84 atoms in group peptide
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#dump 1 peptide atom 10 dump.peptide
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#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
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#dump_modify 2 pad 3
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#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
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#dump_modify 3 pad 3
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#compute bnd all property/local btype batom1 batom2
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#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
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run 300
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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 = 10648 3375
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Neighbor list info ...
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1 neighbor list requests
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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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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 = 15.1545 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
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PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
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E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
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E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
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---------------- Step 50 ----- CPU = 1.0068 (sec) ----------------
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TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
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PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
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E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
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E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7980
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 7.80799e-07
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6 0.997 1.06209e-06
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8 1.08 6.20485e-07
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10 1.111 6.23445e-07
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12 1.08 2.68063e-07
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14 0.96 0
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18 0.957201 5.38018e-06
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31 104.52 0.000502316
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---------------- Step 100 ----- CPU = 2.0247 (sec) ----------------
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TotEng = -5257.9972 KinEng = 1078.0556 Temp = 267.9664
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PotEng = -6336.0528 E_bond = 14.4828 E_angle = 43.4429
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E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
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E_coul = 26786.6841 E_long = -33906.5620 Press = -648.6637
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---------------- Step 150 ----- CPU = 3.0615 (sec) ----------------
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TotEng = -5287.2845 KinEng = 1098.6036 Temp = 273.0739
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PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
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E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9686
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E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1888
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 2.18836e-07
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6 0.997 1.50855e-07
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8 1.08 6.58342e-08
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10 1.111 5.5535e-07
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12 1.08 1.99243e-07
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14 0.96 0
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18 0.957201 3.59666e-06
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31 104.52 0.000388186
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---------------- Step 200 ----- CPU = 4.0675 (sec) ----------------
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TotEng = -5308.4527 KinEng = 1100.5055 Temp = 273.5467
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PotEng = -6408.9582 E_bond = 18.2714 E_angle = 33.3035
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E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3264
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E_coul = 26736.1130 E_long = -33902.3928 Press = -1470.3831
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---------------- Step 250 ----- CPU = 5.1252 (sec) ----------------
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TotEng = -5294.1807 KinEng = 1071.1619 Temp = 266.2529
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PotEng = -6365.3426 E_bond = 14.2022 E_angle = 39.1953
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E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5416
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E_coul = 26713.8467 E_long = -33908.7226 Press = -188.8007
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 3.78262e-06
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6 0.997001 3.50131e-06
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8 1.08 2.0932e-06
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10 1.111 5.64324e-06
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12 1.08 2.10399e-06
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14 0.96 0
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18 0.957202 7.67973e-06
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31 104.52 0.000806336
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---------------- Step 300 ----- CPU = 6.1883 (sec) ----------------
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TotEng = -5251.4333 KinEng = 1123.6266 Temp = 279.2937
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PotEng = -6375.0599 E_bond = 14.2249 E_angle = 38.4712
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E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4550
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E_coul = 26745.4115 E_long = -33909.1249 Press = -469.5254
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Loop time of 6.18835 on 1 procs for 300 steps with 2004 atoms
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Performance: 8.377 ns/day, 2.865 hours/ns, 48.478 timesteps/s
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99.9% 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 | 4.8942 | 4.8942 | 4.8942 | 0.0 | 79.09
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Bond | 0.015213 | 0.015213 | 0.015213 | 0.0 | 0.25
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Kspace | 0.49706 | 0.49706 | 0.49706 | 0.0 | 8.03
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Neigh | 0.67515 | 0.67515 | 0.67515 | 0.0 | 10.91
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Comm | 0.029536 | 0.029536 | 0.029536 | 0.0 | 0.48
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Output | 0.00019145 | 0.00019145 | 0.00019145 | 0.0 | 0.00
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Modify | 0.070009 | 0.070009 | 0.070009 | 0.0 | 1.13
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Other | | 0.006974 | | | 0.11
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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: 11181 ave 11181 max 11181 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 708029 ave 708029 max 708029 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 708029
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Ave neighs/atom = 353.308
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 26
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Dangerous builds = 0
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Total wall time: 0:00:06
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