forked from lijiext/lammps
191 lines
6.9 KiB
Groff
191 lines
6.9 KiB
Groff
LAMMPS (5 Oct 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 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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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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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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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 = 14.8928 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 = -837.0112
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---------------- Step 50 ----- CPU = 0.2741 (sec) ----------------
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TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745
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PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365
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E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785
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E_coul = 26804.4441 E_long = -33907.7003 Press = -1331.7946
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 7.80613e-07
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6 0.997 1.06181e-06
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8 1.08 6.20292e-07
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10 1.111 6.23284e-07
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12 1.08 2.67996e-07
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14 0.96 0
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18 0.957201 5.3796e-06
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31 104.52 0.000502278
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---------------- Step 100 ----- CPU = 0.5371 (sec) ----------------
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TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663
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PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429
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E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273
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E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819
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---------------- Step 150 ----- CPU = 0.8054 (sec) ----------------
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TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737
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PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594
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E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675
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E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1830
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 2.18699e-07
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6 0.997 1.50563e-07
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8 1.08 6.57501e-08
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10 1.111 5.54188e-07
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12 1.08 1.98841e-07
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14 0.96 0
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18 0.957201 3.59627e-06
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31 104.52 0.000388336
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---------------- Step 200 ----- CPU = 1.0652 (sec) ----------------
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TotEng = -5308.4465 KinEng = 1100.4875 Temp = 273.5422
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PotEng = -6408.9340 E_bond = 18.2714 E_angle = 33.3040
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E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221
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E_coul = 26736.1321 E_long = -33902.3837 Press = -1470.3400
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---------------- Step 250 ----- CPU = 1.3409 (sec) ----------------
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TotEng = -5294.1570 KinEng = 1071.0939 Temp = 266.2360
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PotEng = -6365.2509 E_bond = 14.2013 E_angle = 39.1996
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E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4591
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E_coul = 26714.0037 E_long = -33908.7139 Press = -189.6059
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 3.79043e-06
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6 0.997001 3.60519e-06
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8 1.08 2.09368e-06
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10 1.111 5.64839e-06
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12 1.08 2.10676e-06
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14 0.96 0
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18 0.957202 7.72573e-06
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31 104.52 0.000806208
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---------------- Step 300 ----- CPU = 1.6199 (sec) ----------------
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TotEng = -5251.3639 KinEng = 1123.7721 Temp = 279.3299
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PotEng = -6375.1360 E_bond = 14.2206 E_angle = 38.4274
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E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3470
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E_coul = 26745.4071 E_long = -33909.0790 Press = -471.5569
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Loop time of 1.61992 on 4 procs for 300 steps with 2004 atoms
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Performance: 32.002 ns/day, 0.750 hours/ns, 185.194 timesteps/s
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99.8% CPU use with 4 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 | 1.1484 | 1.17 | 1.1865 | 1.5 | 72.23
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Bond | 0.0011752 | 0.003831 | 0.0069602 | 4.0 | 0.24
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Kspace | 0.16316 | 0.1798 | 0.20413 | 3.9 | 11.10
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Neigh | 0.16885 | 0.16895 | 0.16902 | 0.0 | 10.43
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Comm | 0.046479 | 0.047215 | 0.047759 | 0.2 | 2.91
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Output | 0.00024033 | 0.00025702 | 0.00030375 | 0.2 | 0.02
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Modify | 0.04556 | 0.045949 | 0.046353 | 0.2 | 2.84
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Other | | 0.003923 | | | 0.24
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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: 6587.75 ave 6632 max 6548 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 177005 ave 180556 max 170207 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Total # of neighbors = 708020
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Ave neighs/atom = 353.303
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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: 0:00:01
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