1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
|
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 1 by 1 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) = 14.96 | 14.96 | 14.96 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 -0.23916172 0.76630295 3.8009862 4.4066861 -2.2021529 0.1798796
10000 17.553635 -1.2829068 1.1657706 3.9123497 5.0547767 -2.9598952 0.34416632
11000 17.985843 -1.5465483 0.84770758 3.3368358 5.662125 -2.6329553 0.24353243
12000 17.803319 -1.0407393 0.74246545 3.6148795 4.7651004 -2.5084817 0.10619442
13000 18.979266 -1.3899293 0.54141439 2.8249302 4.7550121 -2.5037554 0.11955235
14000 17.009105 -0.79638876 0.94514282 3.8784001 4.5107273 -2.2861709 0.076774568
15000 16.52792 -0.099911028 0.73468109 3.6878436 5.0897919 -2.6694045 0.1846061
16000 18.602333 -1.2207715 0.73683889 3.5724426 4.2967652 -2.1185335 0.14454439
17000 18.548631 -1.4459452 0.87132388 3.1082541 4.4173372 -2.1488103 0.05085499
18000 18.274944 -0.9082365 0.78279222 3.2003259 4.2230915 -2.0279073 0.067678678
19000 18.363395 -1.5446376 0.84278631 3.5192748 4.5827839 -2.3655766 0.16111203
20000 17.92959 -0.78977685 0.83244452 3.3573732 4.5008538 -2.7568218 0.18551385
21000 16.294685 -0.43068016 1.0820062 4.1094083 4.6392086 -2.4608104 0.1504371
22000 17.945194 -1.12622 0.86476498 3.3577152 4.673294 -2.4760964 0.081229709
23000 18.59629 -1.3692394 0.67592321 3.493029 4.5943035 -2.221834 0.13764568
24000 17.636587 -0.46892268 0.59584902 3.2114851 4.7133747 -2.4081857 0.26633414
25000 16.620668 -0.75136289 1.0243884 4.0835198 5.1451753 -2.6824535 0.24777903
26000 18.59225 -1.0967117 0.56177724 3.2556596 4.3523235 -2.4816091 0.1788868
27000 19.188088 -1.871277 0.96616357 3.0120122 4.3122826 -2.2148745 0.10347086
28000 17.912724 -0.90553766 1.1257482 3.2754041 4.2225708 -2.4365707 0.1807316
29000 17.81248 -1.1502128 0.95470623 3.4118416 4.6659831 -2.1613317 0.11462518
30000 17.018989 -0.89064809 0.84950442 4.1712342 4.4636021 -2.3306882 0.15623897
31000 18.547066 -1.5339831 0.89944952 3.3517223 4.7396826 -2.6121868 0.15212539
32000 17.200059 -1.0016932 0.81295912 4.0695758 4.5595904 -2.3605079 0.1387539
33000 17.531814 -0.70849955 0.75743835 3.226091 4.476408 -2.1190694 0.055884538
34000 18.325131 -1.2897672 0.89479605 3.1671187 4.2968993 -1.9697837 0.17312732
35000 18.289817 -1.0149458 0.75194781 3.4275427 4.5914578 -2.3206357 0.12126296
36000 17.111721 -0.59386121 0.84127598 3.5534448 5.0274338 -2.36455 0.090112107
37000 17.748767 -0.91029178 0.77689229 3.8018169 4.7249541 -2.4255194 0.054726961
38000 17.2172 -0.43070288 0.88086005 3.5586613 4.3203841 -2.0587465 0.050764106
39000 18.482481 -0.75351762 0.87677942 2.9007389 4.7178108 -2.6463003 0.25313342
40000 18.465192 -1.4076534 0.92705504 3.3546181 4.4030743 -2.3873054 0.071878288
41000 18.12592 -1.5839327 0.6979962 3.2851401 5.2815413 -2.3054411 0.11390788
42000 18.376705 -1.0077349 0.70647799 2.9499245 4.6421626 -2.3504786 0.17673009
43000 16.929642 -0.72975766 0.90203733 3.7176511 4.7292387 -2.2860424 0.084829761
44000 17.271104 -0.99868378 1.0201679 4.1153184 4.2727269 -2.1172719 0.1029166
45000 18.230889 -1.0093287 0.85777597 2.8550682 4.3913999 -2.0720155 0.073553812
46000 18.241544 -1.7077516 0.95512232 3.8878131 4.3812806 -2.3031674 0.10194331
47000 18.12818 -0.83919194 0.71483948 2.7541388 4.7432398 -2.2644558 0.053413336
48000 17.965762 -0.92946694 0.70540637 3.4567259 4.5010549 -2.3038276 0.15002746
49000 16.815211 0.19052416 1.0076747 3.1045662 4.9638411 -2.3712162 0.1057081
50000 17.193025 -0.89817177 1.2261029 3.7515175 4.4880145 -2.2643247 0.29712734
51000 18.665005 -0.84670757 0.56076732 3.0839868 4.458076 -2.2261738 0.046374416
52000 17.619937 -0.89986585 0.64159147 3.7530936 4.8769799 -2.3791391 0.13429701
53000 16.916466 -0.58872911 0.96495189 3.6755814 4.7419669 -2.3886804 0.20915197
54000 17.199476 -0.88155666 0.64336469 3.927811 4.8019389 -2.2773601 0.18734294
55000 18.158496 -0.81126798 0.68333055 2.9741959 4.4463001 -2.1864535 0.071857857
56000 17.860471 -1.6993 1.2366001 3.7857634 4.7701817 -2.4192649 0.15619688
57000 18.444698 -0.82854071 0.63506471 3.1823771 4.4432216 -2.2987011 0.1407306
58000 18.047238 -1.4404915 1.0095109 3.7328328 4.6385391 -2.1656547 0.068584173
59000 16.990212 -0.81630542 0.73745944 4.2847598 5.1556617 -2.4218952 0.044901478
60000 18.164864 -0.68273809 0.60589655 3.1085907 4.5637459 -2.2379342 0.11464892
61000 17.772457 -1.1890999 0.80411722 3.7218185 4.7750335 -2.4439724 0.11358571
62000 17.192042 -0.095008686 0.71713238 3.2284848 4.9345758 -2.4377098 0.12788027
63000 16.877969 -0.62181425 0.8931036 3.6147379 5.3541158 -2.302381 0.072736635
64000 17.934695 -1.1664658 0.74610888 3.5102215 4.6537266 -2.3495291 0.18818648
65000 17.034947 -0.59670985 0.7590603 3.4896411 5.0725358 -2.3057016 0.067650159
66000 18.259418 -0.57940688 0.55125252 3.2917088 4.4949827 -2.3128319 0.17052154
67000 16.656512 -1.1797815 0.88985636 4.3326457 4.7143632 -2.4187476 0.35820295
68000 18.218359 -0.98502226 0.8053151 2.8694875 4.6774476 -2.2750794 0.027475615
69000 18.591716 -1.2961393 0.85778116 3.4232791 4.3626988 -2.2150059 0.047420611
70000 18.282862 -1.5115081 1.1486318 3.1099158 4.5945816 -2.1742452 0.15701805
71000 17.722244 -1.3606013 0.98913854 3.9050958 4.4617942 -2.1980629 0.16665753
72000 17.578225 -1.0672968 1.1898075 3.3110576 4.6292013 -2.1893929 0.15802869
73000 17.700619 -1.1203382 0.68447774 3.7617044 4.5508307 -2.2031338 0.046795482
74000 18.864586 -1.3377627 0.54243736 3.1047677 4.6094993 -2.2506839 0.0618695
75000 17.252732 -0.75791613 0.79934329 3.6289993 4.8336985 -2.3716023 0.048355835
76000 15.625117 -0.17710917 1.0083339 4.5957493 4.3952808 -2.0145142 0.2165007
77000 18.663599 -1.214034 0.73808593 3.1282966 4.1967921 -2.04274 0.20129707
78000 16.687112 -0.81273153 1.0670946 3.5384094 5.3755076 -2.1922472 0.025711096
79000 18.169502 -1.443215 1.1859821 3.4043489 4.3415317 -2.3447052 0.11854425
80000 18.787124 -1.6654307 1.0501597 3.0298408 4.2077733 -1.9985344 0.26128514
81000 17.807683 -1.3429276 0.83231514 3.8051489 4.659607 -2.3866437 0.20196892
82000 17.331324 -0.78827019 0.95190013 3.7412416 4.3529018 -2.307155 0.073785492
83000 17.597954 -0.36573657 0.84239516 3.1227374 4.5709276 -2.2732398 0.12571923
84000 17.961063 -1.2301714 0.65709128 3.5308724 4.5505295 -2.4116051 0.14784451
85000 18.034924 -1.1445169 1.1114893 3.2704327 4.4570221 -2.3336871 0.084147643
86000 18.35847 -1.0687438 0.71638387 3.2994265 4.7224093 -2.6523985 0.2338977
87000 17.297387 -0.36290631 0.67031988 3.9566445 4.6234059 -2.8008118 0.22786876
88000 17.179923 -0.40756603 1.0448818 3.4777257 4.454146 -2.420876 0.18845717
89000 17.548178 -1.2104623 0.81223923 3.8553959 4.8092953 -2.3606086 0.16057241
90000 18.203445 -1.2476535 0.93776844 3.3519306 4.5880767 -2.3299626 0.13273664
91000 17.577661 -0.9536919 0.98278572 3.6805268 4.269043 -2.2758847 0.16458677
92000 17.249982 -1.2620718 1.2379068 4.077245 4.6893055 -2.3623079 0.080584665
93000 17.263474 -1.1194017 0.56075789 3.9937658 4.9398469 -2.458799 0.1178667
94000 17.794002 -0.94808955 0.82296171 3.4988835 4.723922 -2.4525227 0.093849723
95000 17.380526 -1.3184326 1.2273125 4.01341 4.3749028 -2.1577427 0.12183053
96000 17.421883 -1.0247407 0.98739686 4.1656417 4.5509065 -2.5533884 0.15050166
97000 18.097453 -0.82643049 0.58678318 3.5934164 4.2844244 -2.187686 0.1173314
98000 17.110826 -0.9875292 1.1047966 3.5373119 4.9434687 -2.3951197 0.051018748
99000 17.497671 -0.72505537 1.1343346 3.3335263 4.7133241 -2.3170405 0.18322857
100000 17.502653 -1.2246734 0.85121721 4.132924 4.6912393 -2.605162 0.24425609
Loop time of 2.20757 on 1 procs for 100000 steps with 34 atoms
Performance: 7827.606 ns/day, 0.003 hours/ns, 45298.646 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.80344 | 0.80344 | 0.80344 | 0.0 | 36.39
Bond | 1.0867 | 1.0867 | 1.0867 | 0.0 | 49.22
Neigh | 0.0081377 | 0.0081377 | 0.0081377 | 0.0 | 0.37
Comm | 0.017823 | 0.017823 | 0.017823 | 0.0 | 0.81
Output | 0.0011017 | 0.0011017 | 0.0011017 | 0.0 | 0.05
Modify | 0.21444 | 0.21444 | 0.21444 | 0.0 | 9.71
Other | | 0.07595 | | | 3.44
Nlocal: 34 ave 34 max 34 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 395 ave 395 max 395 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 395
Ave neighs/atom = 11.6176
Ave special neighs/atom = 9.52941
Neighbor list builds = 230
Dangerous builds = 0
Total wall time: 0:00:02
|
