forked from lijiext/lammps
179 lines
6.2 KiB
Groff
179 lines
6.2 KiB
Groff
LAMMPS (30 Apr 2015)
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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 2 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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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 = 4312 960
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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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master list distance cutoff = 12
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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 = 14.4096 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 = 0.2787 (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 = -1331.7981
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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 6.20484e-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 = 0.5603 (sec) ----------------
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TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
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PotEng = -6336.0529 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 = 26786.6840 E_long = -33906.5620 Press = -648.6639
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---------------- Step 150 ----- CPU = 0.8498 (sec) ----------------
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TotEng = -5287.2844 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 = 736.9685
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E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1895
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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 1.50856e-07
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8 1.08 6.58343e-08
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10 1.111 5.55349e-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 0.000388184
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---------------- Step 200 ----- CPU = 1.1308 (sec) ----------------
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TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
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PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
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E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
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E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3871
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---------------- Step 250 ----- CPU = 1.4236 (sec) ----------------
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TotEng = -5294.1809 KinEng = 1071.1623 Temp = 266.2530
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PotEng = -6365.3432 E_bond = 14.2022 E_angle = 39.1953
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E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5412
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E_coul = 26713.8465 E_long = -33908.7226 Press = -188.8077
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 3.78266e-06
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6 0.997001 3.50137e-06
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8 1.08 2.09322e-06
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10 1.111 5.64331e-06
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12 1.08 2.10401e-06
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14 0.96 0
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18 0.957202 7.67991e-06
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31 104.52 0.000806336
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---------------- Step 300 ----- CPU = 1.7191 (sec) ----------------
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TotEng = -5251.4350 KinEng = 1123.6256 Temp = 279.2935
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PotEng = -6375.0606 E_bond = 14.2249 E_angle = 38.4712
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E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4557
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E_coul = 26745.4100 E_long = -33909.1249 Press = -469.5450
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Loop time of 1.71912 on 4 procs for 300 steps with 2004 atoms
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Pair time (%) = 1.23855 (72.0454)
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Bond time (%) = 0.0039109 (0.227494)
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Kspce time (%) = 0.17904 (10.4146)
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Neigh time (%) = 0.169081 (9.83531)
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Comm time (%) = 0.0679622 (3.95331)
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Outpt time (%) = 0.000325799 (0.0189515)
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Other time (%) = 0.0602537 (3.50491)
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Nlocal: 501 ave 508 max 490 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Nghost: 6586.25 ave 6628 max 6548 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 177007 ave 180562 max 170212 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Total # of neighbors = 708028
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Ave neighs/atom = 353.307
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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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