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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
units real
neigh_modify delay 2 every 1
#newton off
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
improper_style harmonic
pair_style lj/charmmfsw/coul/charmmfsh 8 12
Switching to CHARMM coulomb energy conversion constant (src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp:55)
pair_modify mix arithmetic
fix cmap all cmap charmm22.cmap
Reading potential file charmm22.cmap with DATE: 2016-09-26
fix_modify cmap energy yes
read_data gagg.data fix cmap crossterm CMAP
orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
1 by 2 by 2 MPI processor grid
reading atoms ...
34 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
33 bonds
reading angles ...
57 angles
reading dihedrals ...
75 dihedrals
reading impropers ...
7 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
13 = max # of 1-4 neighbors
16 = max # of special neighbors
special_bonds charmm
fix 1 all nve
#fix 1 all nvt temp 300 300 100.0
#fix 2 all shake 1e-9 500 0 m 1.0
velocity all create 0.0 12345678 dist uniform
thermo 1000
thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
timestep 2.0
run 100000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmmfsw/coul/charmmfsh, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 14.94 | 15.57 | 16.2 Mbytes
Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
0 16.28796 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
1000 18.817034 -0.84376064 0.78927748 2.7554954 4.4369572 -2.7762224 0.12700913
2000 18.091506 -1.0458619 0.72328506 3.0956514 4.6724302 -2.3582544 0.22717594
3000 17.841047 -1.2177066 0.72658478 2.6693344 5.4322049 -2.0735857 0.075472354
4000 16.203768 -0.43010212 0.99813471 3.9020929 5.2015958 -2.562376 0.17393693
5000 17.74278 -0.58387686 0.9095749 3.4440437 4.5474453 -2.3771369 0.12369887
6000 18.84065 -1.5987004 0.81046711 2.9214019 4.5243733 -2.3180496 0.12365723
7000 18.84546 -0.96510756 0.57164583 3.0069325 4.6579161 -2.8966842 0.186473
8000 16.965729 -0.85937109 0.62698075 3.6416157 5.2427548 -2.4812956 0.14018019
9000 16.847152 -0.23916171 0.76630294 3.8009862 4.406686 -2.2021529 0.17987959
10000 17.553634 -1.2829064 1.1657706 3.91235 5.0547763 -2.9598949 0.34416627
11000 17.985844 -1.546548 0.84770734 3.3368355 5.6621242 -2.6329556 0.24353209
12000 17.803315 -1.0407428 0.74246591 3.6148861 4.7651023 -2.5084818 0.10619443
13000 18.979298 -1.3899069 0.54140353 2.824908 4.7549927 -2.5037439 0.1195534
14000 17.009076 -0.79641495 0.94514807 3.8784683 4.5107542 -2.2861686 0.076775119
15000 16.527651 -0.10009622 0.73467885 3.6878968 5.0899041 -2.6692893 0.18460865
16000 18.604151 -1.2210802 0.73655927 3.5718605 4.2964962 -2.1189359 0.14449313
17000 18.546852 -1.4467993 0.87198724 3.1105181 4.4184817 -2.1495741 0.051004484
18000 18.269987 -0.90581341 0.7831269 3.2002375 4.2239607 -2.0289403 0.067912952
19000 18.365165 -1.5425052 0.84132905 3.5171046 4.582444 -2.3624811 0.15993488
20000 17.919207 -0.79257338 0.83410115 3.3693164 4.4968189 -2.7465541 0.1841698
21000 16.278922 -0.44214815 1.0902282 4.1142335 4.6450522 -2.4508096 0.14648872
22000 17.980488 -1.1391025 0.8652074 3.3488636 4.6605505 -2.4768211 0.082465921
23000 18.89971 -1.3694963 0.64862919 3.3841726 4.4302445 -2.2592268 0.13555028
24000 17.161166 -0.55945806 0.69448645 3.4675689 5.0748468 -2.5837022 0.2986302
25000 17.156172 -0.68212797 0.95625815 3.9473369 4.6696376 -2.597154 0.27829376
26000 17.825866 -0.73781842 0.75572313 3.303994 4.6064489 -2.4678257 0.1101394
27000 18.616198 -1.1970872 0.74929218 2.7266748 4.5928796 -2.3031488 0.10452726
28000 17.263879 -1.1343882 1.3560474 3.5869107 4.954875 -2.3468498 0.055318117
29000 18.218484 -0.64810872 0.68572616 3.3763474 4.5347093 -2.5532561 0.044134638
30000 17.213834 -1.1463665 0.81650849 4.5021522 4.5992871 -2.40695 0.04205291
31000 17.8559 -0.99467757 0.71511439 3.5755686 4.9305642 -2.6691079 0.15067927
32000 17.632612 -0.8302854 1.2248328 3.4735959 4.6212801 -2.7231143 0.34288338
33000 17.176657 -0.64567669 0.97026796 3.3935778 4.5587216 -2.2673303 0.14591296
34000 17.928014 -0.78865694 0.54309368 3.508016 4.7763531 -2.4383684 0.18688827
35000 17.961344 -1.3258434 0.79791264 3.6021659 4.7174496 -2.4153924 0.14281974
36000 17.363519 -0.87152419 0.86057615 3.9176779 4.3965038 -2.1041204 0.12738842
37000 16.06135 -1.0007854 1.3152379 4.9256357 4.4181047 -2.2698823 0.20913478
38000 16.980479 -0.95646429 0.81311125 3.9783382 5.1047807 -2.5399437 0.20183215
39000 18.494869 -0.90369184 0.71368 2.9713413 4.7252974 -2.4204755 0.15716213
40000 17.879106 -0.86166372 0.89882312 3.4726397 4.3971385 -2.3460741 0.13021249
41000 18.035763 -1.2809432 0.91931903 3.4005222 4.5201606 -2.411653 0.10482408
42000 17.688254 -1.0984284 0.93541053 3.723003 4.6284132 -2.2978157 0.098932073
43000 17.162211 -1.2347977 1.0781323 4.0892528 4.6269303 -2.3550598 0.05480233
44000 17.368788 -0.62753591 0.95568557 3.2537525 4.6683551 -2.316093 0.17116275
45000 17.28803 -0.76881568 0.92524577 3.6089685 4.3707256 -2.2940853 0.054227805
46000 17.659642 -1.0636933 0.62134856 3.7988149 4.642663 -2.2567824 0.059618876
47000 17.520356 -0.73678104 0.65813025 3.5138815 4.6758778 -2.2989321 0.099899312
48000 16.812802 -0.88677379 0.9634123 3.5723247 5.1067533 -2.3228969 0.1375947
49000 16.689302 -0.84108162 0.97663708 4.5288711 4.2042907 -2.0960932 0.12712083
50000 17.34708 -0.99417589 0.74282621 4.0884892 4.4655725 -2.3445562 0.040137606
51000 18.386747 -1.4258618 0.7415682 3.5702618 4.3472793 -2.3531028 0.076627832
52000 18.62586 -1.3545312 0.8226399 2.8749248 4.6581056 -2.1415891 0.074885964
53000 18.142099 -1.0903937 1.0355955 3.39219 4.3761473 -2.3714216 0.12991324
54000 18.452949 -1.2117507 0.79702906 3.0176388 4.4872416 -2.3195176 0.073698473
55000 17.317369 -0.89629461 0.7135235 4.0285995 4.8471482 -2.3306208 0.067829904
56000 17.331139 -0.70400555 0.92933471 3.1428751 5.1938451 -2.3960347 0.10207963
57000 17.769688 -0.69097945 0.6761737 3.6233451 4.3309071 -2.588033 0.33444943
58000 17.808019 -0.50062525 0.84330344 3.0780006 4.4191107 -2.2626852 0.23176683
59000 16.974427 -0.22275961 1.1171381 3.6002905 4.8457806 -2.4506404 0.086485736
60000 18.426097 -1.1640712 0.89526359 3.0738119 4.3475275 -2.2585607 0.17344541
61000 18.347861 -1.1389796 0.94799071 3.3858595 4.3778565 -2.4264935 0.022565214
62000 17.472407 -0.054270199 0.78119769 3.5192829 4.5922308 -2.7152004 0.077668809
63000 18.451352 -0.99265328 0.65501446 3.1607389 4.4871585 -2.3972756 0.1095194
64000 17.664837 -1.3148668 0.94502551 3.7697825 4.6332111 -2.4479629 0.2841013
65000 17.857844 -0.82183909 0.94533467 3.3987595 4.7509642 -2.9322189 0.15667848
66000 16.809282 -0.11096144 0.79005552 4.2974065 4.667357 -2.85833 0.08678995
67000 18.331716 -0.77668223 0.85848669 2.630497 4.6984372 -2.6328844 0.20335427
68000 17.818595 -0.93709899 0.87885516 3.3973927 4.4542279 -2.2667437 0.18791512
69000 18.115509 -1.440213 1.347904 3.3737104 4.3392351 -2.3748603 0.15273089
70000 17.230663 -0.76722679 0.77580436 3.920298 4.3064374 -2.057197 0.1064338
71000 17.972819 -0.56240735 0.69337989 3.2513062 4.5245288 -2.5597279 0.27216928
72000 18.432872 -1.3313091 0.84535471 3.1727393 4.483952 -2.4128395 0.1378963
73000 17.697723 -0.97837773 1.0529842 3.8074009 4.72378 -2.7174621 0.17825868
74000 18.504521 -1.1231346 0.88277801 3.0479334 4.3481094 -2.2732739 0.086093125
75000 17.934978 -1.4213334 0.9145673 3.8583169 4.5864462 -2.3243695 0.081450732
76000 18.508287 -0.98310739 0.64131006 3.2474703 4.4350548 -2.2768941 0.11216496
77000 16.846831 -1.1997156 0.97525037 4.5115234 4.4822983 -2.2271894 0.15009063
78000 18.298764 -0.89093904 1.151268 2.9546969 4.5531473 -2.6022807 0.17136053
79000 17.440102 -0.84471365 0.79902079 3.7146172 4.5874272 -2.3161711 0.074592893
80000 16.96787 -0.76797183 1.1525337 3.4597685 5.140513 -2.6897182 0.21382322
81000 17.081167 -1.0035883 0.9417994 4.3325391 4.7180405 -2.6083103 0.19511734
82000 16.507622 -1.05195 1.1260094 4.2926577 4.7646789 -2.4006964 0.14462259
83000 17.693074 -0.86921671 0.78469232 3.2635421 4.7625581 -2.1472473 0.089898176
84000 17.485199 -0.63086362 0.84462236 3.7419011 4.3478352 -2.2855255 0.12993625
85000 17.791978 -1.2653364 0.83896065 3.8569475 4.7233956 -2.4464365 0.10326311
86000 17.859089 -0.81401354 0.81139105 3.4899076 4.5074402 -2.3756207 0.13928587
87000 17.922335 -1.381674 1.1201002 4.0246458 4.8013529 -3.0706282 0.14319694
88000 17.891848 -1.1065441 0.95945646 3.8687633 4.2747388 -2.2353028 0.2196999
89000 17.618833 -0.74803168 1.0695045 2.8694377 4.9185961 -2.2867946 0.14163937
90000 18.321207 -1.332528 0.81671672 3.921007 4.2555562 -2.4712797 0.071633057
91000 18.553104 -1.3004122 0.9317915 3.1911912 4.3221185 -2.2542173 0.090485864
92000 17.39548 -0.87272071 0.96671708 3.8750471 4.3904352 -2.5461358 0.1301959
93000 17.706773 -1.0859407 0.96681042 3.5302332 4.5674911 -2.2899428 0.051797638
94000 18.315271 -1.0896814 0.82594056 3.253212 4.6972747 -2.3528794 0.14073237
95000 17.512959 -1.2251671 1.1726435 3.870858 4.2950784 -2.3334602 0.063946067
96000 17.196402 -1.350795 1.0149203 4.5463081 4.46194 -2.2969009 0.057997074
97000 18.119424 -1.1822278 1.0710466 2.9669136 4.5028366 -2.3136825 0.10116804
98000 18.611528 -1.1675308 0.86166718 3.8663186 4.5385301 -3.2887663 0.17772415
99000 17.221377 -0.72476724 1.0463603 3.2816006 4.9591142 -2.6471303 0.23335447
100000 17.500556 -1.0148716 1.2155656 3.5359122 4.5111603 -2.2594507 0.14328565
Loop time of 2.16745 on 4 procs for 100000 steps with 34 atoms
Performance: 7972.502 ns/day, 0.003 hours/ns, 46137.167 timesteps/s
94.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.058708 | 0.22252 | 0.54183 | 40.5 | 10.27
Bond | 0.038348 | 0.31503 | 0.66653 | 48.0 | 14.53
Neigh | 0.0070002 | 0.007808 | 0.0096803 | 1.2 | 0.36
Comm | 0.42884 | 1.1121 | 1.5566 | 42.8 | 51.31
Output | 0.002564 | 0.0036213 | 0.0063593 | 2.6 | 0.17
Modify | 0.036094 | 0.12956 | 0.22792 | 25.9 | 5.98
Other | | 0.3768 | | | 17.38
Nlocal: 8.5 ave 15 max 2 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 25.5 ave 32 max 19 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 98.75 ave 271 max 18 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 395
Ave neighs/atom = 11.6176
Ave special neighs/atom = 9.52941
Neighbor list builds = 236
Dangerous builds = 0
Total wall time: 0:00:02
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