forked from lijiext/lammps
update cmap example logfiles
This commit is contained in:
Axel Kohlmeyer
parent
2ed90c1669
commit
d0a83e9e12
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@ -1,205 +0,0 @@
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LAMMPS (31 Mar 2017)
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# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
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units real
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neigh_modify delay 2 every 1
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#newton off
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmmfsw
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improper_style harmonic
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pair_style lj/charmmfsw/coul/charmmfsh 8 12
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pair_modify mix arithmetic
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fix cmap all cmap charmm22.cmap
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Reading potential file charmm22.cmap with DATE: 2016-09-26
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fix_modify cmap energy yes
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read_data gagg.data fix cmap crossterm CMAP
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orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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34 atoms
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scanning bonds ...
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4 = 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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12 = 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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33 bonds
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reading angles ...
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57 angles
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reading dihedrals ...
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75 dihedrals
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reading impropers ...
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7 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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13 = max # of 1-4 neighbors
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16 = max # of special neighbors
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special_bonds charmm
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fix 1 all nve
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#fix 1 all nvt temp 300 300 100.0
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#fix 2 all shake 1e-9 500 0 m 1.0
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velocity all create 0.0 12345678 dist uniform
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thermo 1000
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thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
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timestep 2.0
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run 100000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 12 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmmfsw/coul/charmmfsh, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 14.96 | 14.96 | 14.96 Mbytes
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Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
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0 16.287573 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
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1000 18.816462 -0.84379243 0.78931817 2.7554247 4.4371421 -2.7762038 0.12697656
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2000 18.091571 -1.045888 0.72306589 3.0951524 4.6725102 -2.3580092 0.22712496
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3000 17.835596 -1.2171641 0.72666403 2.6696491 5.4373798 -2.0737041 0.075101693
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4000 16.211232 -0.42713611 0.99472642 3.8961462 5.2009895 -2.5626866 0.17356243
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5000 17.72183 -0.57081189 0.90733068 3.4376382 4.5457582 -2.3727543 0.12354518
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6000 18.753977 -1.5772499 0.81468321 2.9236782 4.6033216 -2.3380859 0.12835782
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7000 18.186024 -0.84205608 0.58996182 3.0329585 4.7221473 -2.5733243 0.10047631
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8000 18.214306 -1.1360938 0.72597611 3.7493028 4.7319958 -2.8957969 0.2006046
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9000 17.248408 -0.48641993 0.90266229 2.9721743 4.7651056 -2.1473354 0.1302043
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10000 17.760655 -1.2968444 0.92384663 3.7007455 4.7378947 -2.2147779 0.06940579
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11000 17.633929 -0.57368413 0.84872849 3.4277114 4.285393 -2.236944 0.17204973
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12000 18.305835 -1.0675148 0.75879532 2.8853173 4.685027 -2.409087 0.087538866
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13000 17.391558 -0.9975291 0.66671947 3.8065638 5.2285578 -2.4198822 0.06253594
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14000 17.483387 -0.67727643 0.91966477 3.7317031 4.7770445 -2.6080027 0.11487095
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15000 18.131749 -1.1918751 1.0025684 3.1238131 4.789742 -2.2546745 0.13782813
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16000 16.972343 -0.43926531 0.60644597 3.7551592 4.8658618 -2.2627659 0.12353145
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17000 18.080785 -1.2073565 0.7867072 3.5671106 4.43754 -2.5092904 0.17429146
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18000 17.474576 -0.97836065 0.8678524 3.7961537 4.3409032 -1.8922572 0.134048
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19000 17.000911 -1.2286864 0.83615834 3.9322908 4.9319492 -2.3281576 0.056689619
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20000 17.043286 -0.8506561 0.80966589 3.5087339 4.8603878 -2.3365263 0.096794824
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21000 17.314495 -1.1430889 0.95363892 4.2446032 4.2756745 -2.1829483 0.17119518
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22000 18.954881 -0.998673 0.58688334 2.71536 4.6634319 -2.6862804 0.20328442
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23000 17.160427 -0.97803282 0.86894041 4.0897736 4.3146238 -2.1962289 0.075339092
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24000 17.602026 -1.0833323 0.94888776 3.7341878 4.3084335 -2.1640414 0.081493681
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25000 17.845584 -1.3432612 0.93497086 3.8911043 4.468032 -2.3475883 0.093204333
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26000 17.833261 -1.1020534 0.77931087 3.7628141 4.512381 -2.3134761 0.15568465
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27000 17.68607 -1.3222026 1.1985872 3.5817624 4.6360755 -2.3492774 0.08427906
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28000 18.326649 -1.2669291 0.74809075 3.2624429 4.4698564 -2.3679076 0.14677293
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29000 17.720933 -1.0773886 0.83099482 3.7652834 4.6584594 -2.8255303 0.23092596
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30000 18.201999 -1.0168706 1.0637455 3.453095 4.3738593 -2.8063214 0.18658217
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31000 17.823502 -1.2685768 0.84805585 3.8600661 4.2195821 -2.1169716 0.12517101
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32000 16.883133 -0.62062648 0.84434922 3.5042683 5.1264906 -2.2674699 0.030138165
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33000 17.805715 -1.679553 1.2430372 4.314677 4.2523894 -2.3008321 0.18591872
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34000 16.723767 -0.54189072 1.1282827 3.8542159 4.3026559 -2.2186336 0.05392425
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35000 17.976909 -0.72092075 0.5876319 2.9726396 5.0881439 -2.491692 0.17356291
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36000 18.782492 -1.514246 0.63237955 3.2777164 4.6077164 -2.502574 0.082537318
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37000 17.247716 -0.6344626 0.79885976 3.452491 4.7618281 -2.3902444 0.11450271
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38000 17.996494 -1.6712877 1.0111769 4.1689136 4.46963 -2.4076725 0.11875756
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39000 17.586857 -0.74508086 0.95970486 3.7395038 4.6011357 -2.9854953 0.30143284
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40000 17.494879 -0.30772446 0.72047991 3.2604877 4.7283734 -2.3812495 0.16399034
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41000 15.855772 -0.49642605 0.82496448 4.5139653 4.76884 -2.214141 0.10899661
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42000 17.898568 -1.3078863 1.1505144 4.0429873 4.3889581 -2.8696559 0.23336417
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43000 19.014372 -1.6325979 1.1553166 3.5660772 4.4047997 -2.9302044 0.13672127
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44000 18.250782 -0.97211613 0.72714301 3.2258362 4.7257298 -2.5533613 0.11968073
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45000 17.335174 0.24746331 1.0415866 3.3220992 4.5251095 -3.0415216 0.24453084
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46000 17.72846 -0.9541418 0.88153841 3.7893452 4.5251883 -2.4003613 0.051809816
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47000 18.226762 -0.67057787 0.84352989 3.0609522 4.5449078 -2.4694254 0.073703949
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48000 17.838074 -0.88768441 1.3812262 3.5890492 4.5827868 -3.0137515 0.21417113
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49000 17.973733 -0.75118705 0.69667886 3.3989025 4.7058886 -2.8243945 0.26665792
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50000 17.461583 -0.65040016 0.68943524 2.9374743 5.6971777 -2.4438011 0.1697603
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51000 16.79766 -0.010684434 0.89795555 3.959039 4.56763 -2.5101098 0.15048853
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52000 17.566543 -0.7262764 0.74354418 3.3423185 4.8426523 -2.4187649 0.16908776
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53000 17.964274 -0.9270914 1.065952 3.0397181 4.4682262 -2.2179503 0.07873406
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54000 17.941256 -0.5807578 0.76516121 3.7262371 4.6975126 -3.179899 0.24433708
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55000 17.079478 -0.48559832 0.95364453 3.0414645 5.2811414 -2.7064882 0.30102814
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56000 17.632179 -0.75403299 0.97577942 3.3672363 4.4851336 -2.3683659 0.051117638
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57000 16.17128 -0.44699325 0.76341543 4.267716 5.0881056 -2.4122329 0.16671692
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58000 16.899276 -0.76481024 1.0400825 3.973493 4.8823309 -2.4270284 0.048716383
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59000 18.145412 -0.84968335 0.71698306 3.2024358 4.6115739 -2.2520353 0.19466966
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60000 17.578258 -1.0067331 0.72822527 3.5375208 4.9110255 -2.2319607 0.11922362
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61000 17.434762 -1.0244393 0.90593099 3.8446915 4.8571191 -2.6228357 0.23259208
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62000 17.580489 -1.1135917 0.79577432 3.7043524 4.6058114 -2.351492 0.042904152
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63000 18.207335 -1.1512268 0.82684507 3.4114738 4.351069 -2.1878441 0.082922105
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64000 18.333083 -1.1182287 0.74058959 3.6905164 4.3226172 -2.7110393 0.14721704
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65000 16.271579 -0.7122151 1.0200168 4.6983643 4.3681131 -2.194921 0.12831024
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66000 17.316444 -0.5729385 0.85254108 3.5769963 4.5526705 -2.3321328 0.040452643
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67000 17.19011 -0.8814312 1.1381258 3.8605789 4.4183813 -2.299607 0.091527355
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68000 18.223367 -1.362189 0.74472056 3.259165 4.486512 -2.2181134 0.048952796
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69000 17.646348 -0.91647162 0.73990335 3.9313692 5.2663097 -3.3816778 0.27769877
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70000 18.173493 -1.3107718 0.96484426 3.219728 4.5045124 -2.3349534 0.082327407
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71000 17.0627 -0.58509083 0.85964129 3.8490884 4.437895 -2.1673348 0.24151404
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72000 17.809764 -0.35128902 0.65479258 3.3945008 4.6160508 -2.5486166 0.10829531
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73000 18.27769 -1.0739758 0.80890957 3.6070901 4.6256762 -2.4576547 0.080025736
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74000 18.109437 -1.0691837 0.66679323 3.5923203 4.4825716 -2.5048169 0.21372319
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75000 17.914569 -1.3500765 1.2993494 3.362421 4.4160377 -2.1278163 0.19397641
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76000 16.563928 -0.16539261 1.0067302 3.5742755 4.8581915 -2.1362429 0.059822408
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77000 18.130477 -0.38361279 0.43406954 3.4725995 4.7005855 -2.8836242 0.11958174
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78000 16.746204 -1.1732959 0.7455507 3.6296638 5.6344113 -2.459208 0.16099803
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79000 18.243999 -1.5850155 1.0108545 3.4727867 4.3367411 -2.316686 0.070480814
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80000 16.960715 -0.84100929 0.91604996 3.862215 4.780949 -2.3711596 0.073916605
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81000 17.697722 -1.1126605 0.952804 3.7114455 4.4216316 -2.2770085 0.091372066
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82000 17.835901 -1.3091474 0.71867629 3.8168122 5.0150205 -2.4730634 0.062592852
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83000 19.168418 -1.476938 0.75592316 3.2304519 4.3946471 -2.2991395 0.13083324
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84000 17.945778 -1.5223622 1.0859941 3.4334011 5.0286682 -2.7550892 0.2476269
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85000 17.950251 -0.85843846 0.86888218 3.3101287 4.5511879 -2.3640013 0.12080834
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86000 17.480699 -0.97493649 0.85049761 3.4973085 4.6344922 -2.343121 0.2009677
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87000 17.980244 -1.114983 0.88796989 3.4113329 4.3535853 -2.2535412 0.14494917
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88000 18.023866 -1.226683 0.62339706 3.7649269 4.5923973 -2.3923523 0.10464375
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89000 16.362829 -0.311462 1.0265375 4.0101723 4.4184777 -2.0314129 0.056570704
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90000 17.533149 -0.41526788 1.0362029 3.4247412 4.2734431 -2.4776658 0.16960663
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91000 17.719099 -1.1956801 1.0069945 3.2380672 4.8982805 -2.2154906 0.12950936
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92000 17.762654 -1.170027 0.95814525 3.5217717 4.5405343 -2.5983677 0.15037754
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93000 17.393958 -0.45641026 0.6579069 3.6002204 4.5942053 -2.5559641 0.12026544
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94000 16.8182 -0.92962066 0.86801362 4.2914398 4.659848 -2.5251987 0.18000415
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95000 17.642086 -0.7994896 0.7003756 3.8036697 4.5252487 -2.4166307 0.15686517
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96000 18.114292 -1.5102104 1.2635908 3.2764427 5.0659496 -2.2777806 0.054309645
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97000 18.575765 -1.6015311 0.69500699 3.1649317 4.9945742 -2.4012125 0.067373724
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98000 16.578893 -0.78030229 0.91524222 4.4429655 4.4622392 -2.4052655 0.15355705
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99000 17.26063 -0.57832833 0.7098846 3.9000046 4.5576484 -2.5333026 0.25517222
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100000 18.377235 -0.89109577 0.68988617 2.8751751 4.4115591 -2.3560731 0.12185212
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Loop time of 2.96043 on 1 procs for 100000 steps with 34 atoms
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Performance: 5836.990 ns/day, 0.004 hours/ns, 33778.875 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 | 1.074 | 1.074 | 1.074 | 0.0 | 36.28
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Bond | 1.6497 | 1.6497 | 1.6497 | 0.0 | 55.72
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Neigh | 0.007576 | 0.007576 | 0.007576 | 0.0 | 0.26
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Comm | 0.012847 | 0.012847 | 0.012847 | 0.0 | 0.43
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Output | 0.0010746 | 0.0010746 | 0.0010746 | 0.0 | 0.04
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Modify | 0.16485 | 0.16485 | 0.16485 | 0.0 | 5.57
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Other | | 0.05037 | | | 1.70
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Nlocal: 34 ave 34 max 34 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 395 ave 395 max 395 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 395
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Ave neighs/atom = 11.6176
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Ave special neighs/atom = 9.52941
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Neighbor list builds = 253
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Dangerous builds = 0
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Total wall time: 0:00:02
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@ -1,205 +0,0 @@
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LAMMPS (31 Mar 2017)
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# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
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units real
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neigh_modify delay 2 every 1
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#newton off
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmmfsw
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improper_style harmonic
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pair_style lj/charmmfsw/coul/charmmfsh 8 12
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pair_modify mix arithmetic
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fix cmap all cmap charmm22.cmap
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Reading potential file charmm22.cmap with DATE: 2016-09-26
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fix_modify cmap energy yes
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read_data gagg.data fix cmap crossterm CMAP
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orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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34 atoms
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scanning bonds ...
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4 = 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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12 = 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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33 bonds
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reading angles ...
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57 angles
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reading dihedrals ...
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75 dihedrals
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reading impropers ...
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7 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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13 = max # of 1-4 neighbors
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16 = max # of special neighbors
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special_bonds charmm
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fix 1 all nve
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#fix 1 all nvt temp 300 300 100.0
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#fix 2 all shake 1e-9 500 0 m 1.0
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velocity all create 0.0 12345678 dist uniform
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thermo 1000
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thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
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timestep 2.0
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run 100000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 12 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmmfsw/coul/charmmfsh, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 14.94 | 15.57 | 16.2 Mbytes
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Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
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0 16.287573 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
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1000 18.816462 -0.84379243 0.78931817 2.7554247 4.4371421 -2.7762038 0.12697656
|
||||
2000 18.091571 -1.045888 0.72306589 3.0951524 4.6725102 -2.3580092 0.22712496
|
||||
3000 17.835596 -1.2171641 0.72666403 2.6696491 5.4373798 -2.0737041 0.075101693
|
||||
4000 16.211232 -0.42713611 0.99472642 3.8961462 5.2009895 -2.5626866 0.17356243
|
||||
5000 17.72183 -0.57081189 0.90733068 3.4376382 4.5457582 -2.3727543 0.12354518
|
||||
6000 18.753977 -1.5772499 0.81468321 2.9236782 4.6033216 -2.3380859 0.12835782
|
||||
7000 18.186024 -0.84205609 0.58996181 3.0329584 4.7221473 -2.5733244 0.10047631
|
||||
8000 18.214306 -1.1360934 0.72597583 3.7493032 4.7319959 -2.8957975 0.20060467
|
||||
9000 17.248415 -0.48642024 0.90266262 2.9721744 4.7651003 -2.1473349 0.13020438
|
||||
10000 17.760663 -1.2968458 0.92384687 3.7007432 4.7378917 -2.2147799 0.06940514
|
||||
11000 17.63395 -0.57366075 0.84871737 3.4276851 4.2853865 -2.2369491 0.17205075
|
||||
12000 18.305713 -1.0672299 0.75876262 2.8852171 4.6850229 -2.4090072 0.087568888
|
||||
13000 17.383367 -0.99678627 0.66712651 3.8060954 5.233865 -2.4180629 0.062014239
|
||||
14000 17.510901 -0.68723297 0.92448551 3.7550867 4.7321218 -2.6059088 0.11504409
|
||||
15000 18.080165 -1.13316 0.99982253 3.09947 4.8171402 -2.2713372 0.14580371
|
||||
16000 17.383245 -0.4535296 0.57826268 3.6453593 4.6541138 -2.2434512 0.13285609
|
||||
17000 17.111153 -0.3414839 0.73667584 3.7485311 4.6262965 -2.6166049 0.12635815
|
||||
18000 16.862046 -1.3592061 1.2371142 4.4878937 4.2937117 -2.2112584 0.066145125
|
||||
19000 18.313891 -1.654238 0.90644101 3.3934089 4.550735 -2.1862171 0.081267736
|
||||
20000 19.083561 -1.3081747 0.56257812 2.7633848 4.6211438 -2.5196707 0.13763071
|
||||
21000 18.23741 -1.051353 0.64408722 3.1735565 4.6912533 -2.2491947 0.099394904
|
||||
22000 17.914515 -0.89769621 0.61793801 3.1224992 4.8683543 -2.282475 0.14524537
|
||||
23000 16.756122 -0.98277883 1.2554905 3.7916115 4.7301443 -2.3094994 0.10226772
|
||||
24000 16.109857 -0.54593177 0.86934462 4.4293574 4.926985 -2.2652264 0.11414331
|
||||
25000 18.590559 -1.497327 1.1898361 2.9134403 4.7854107 -2.4437918 0.067416154
|
||||
26000 18.493391 -1.0533797 0.4889578 3.6563013 4.6171721 -2.3240835 0.11607829
|
||||
27000 18.646522 -1.1229601 0.67956815 2.7937638 4.8991207 -2.4068997 0.10109147
|
||||
28000 18.545103 -1.7237438 0.72488022 3.8041665 4.6459974 -2.4339333 0.21943258
|
||||
29000 17.840505 -1.0909667 0.88133248 3.3698456 5.0311644 -2.5116617 0.08102693
|
||||
30000 17.649527 -0.65409177 0.86781692 3.24112 4.9903073 -2.6234925 0.14799777
|
||||
31000 18.156812 -0.77476556 0.83192789 2.9620784 4.9160635 -2.8571635 0.22283201
|
||||
32000 18.251583 -1.3384075 0.8059007 3.2588176 4.4365328 -2.1875071 0.087883637
|
||||
33000 17.702785 -0.88311587 0.98573641 3.4645713 4.2650091 -2.0909158 0.14233004
|
||||
34000 17.123413 -1.4873429 1.0419563 4.2628178 4.6318762 -2.2292095 0.105354
|
||||
35000 18.162061 -1.0136007 0.82436129 3.6365024 4.5801677 -2.6856989 0.28648222
|
||||
36000 17.65618 -1.094718 0.8872444 3.5075241 4.6382423 -2.3895134 0.18116961
|
||||
37000 17.336475 -1.0657995 0.98869254 3.9252927 4.4383632 -2.2048244 0.22285949
|
||||
38000 17.369467 -0.97623132 0.6712095 4.1349304 4.597754 -2.4088341 0.14608514
|
||||
39000 18.170206 -1.2344285 0.77546195 3.6451049 4.7482287 -2.9895286 0.25768859
|
||||
40000 16.210866 -0.81407781 0.99246271 4.2676233 5.0253763 -2.2929865 0.13348624
|
||||
41000 17.641798 -1.0868157 0.80119513 3.4302526 5.280872 -2.4025406 0.22747391
|
||||
42000 18.349848 -1.613759 1.1497004 3.7800682 4.3237683 -2.8676401 0.2120425
|
||||
43000 19.130245 -1.196778 0.71845659 2.9325758 4.3684415 -2.433424 0.12240982
|
||||
44000 18.061321 -1.2410101 1.0329373 3.0751569 4.7138313 -2.2880904 0.075814461
|
||||
45000 18.162713 -1.4414622 1.009159 4.2298758 4.589593 -2.8502298 0.21606844
|
||||
46000 18.591574 -0.99730412 1.0955215 3.3965004 4.359466 -3.1049731 0.17322629
|
||||
47000 18.380259 -1.2717381 0.72291269 3.3958016 4.6099628 -2.4605065 0.19825185
|
||||
48000 18.130478 -1.5051279 1.2087492 3.2488529 4.6690881 -2.2518174 0.05633061
|
||||
49000 16.419912 -0.89320635 0.98926144 4.0388252 4.9919488 -2.1699511 0.15646479
|
||||
50000 16.453196 -1.0433497 0.778346 4.6078069 4.7320614 -2.3760788 0.17161976
|
||||
51000 18.245221 -0.89550444 0.9310446 3.0758194 4.3944595 -2.3082379 0.19983428
|
||||
52000 17.839632 -1.0221781 0.76425017 3.3331547 4.5368437 -2.0988773 0.21098435
|
||||
53000 18.693035 -1.4231915 0.76333082 3.1612761 4.583242 -2.4485762 0.089191206
|
||||
54000 16.334672 -0.36309884 1.0200365 4.6700448 4.1628702 -2.1713841 0.11431995
|
||||
55000 17.33842 -0.61522682 0.89847366 3.4970659 4.673495 -2.4743036 0.068004878
|
||||
56000 17.790294 -1.0150845 0.73697112 3.6000297 4.5988343 -2.4822509 0.11434632
|
||||
57000 18.913486 -1.0985507 1.0231848 2.7483267 4.4421755 -2.574424 0.1763388
|
||||
58000 17.586896 -0.98284126 0.96965633 3.3330357 4.5325543 -2.1936869 0.083230915
|
||||
59000 17.77788 -1.1649953 0.83092298 3.8004148 4.3940176 -2.3136642 0.017207608
|
||||
60000 17.013042 -0.21728023 1.1688832 3.5374476 4.5462244 -2.4425301 0.15028297
|
||||
61000 17.236242 -1.1342147 1.0301086 3.685948 4.6842331 -2.328108 0.070210812
|
||||
62000 17.529852 -1.2961547 1.0323133 3.4474598 5.1435839 -2.4553423 0.060842687
|
||||
63000 18.754704 -1.1816999 0.51806039 3.140172 4.5832701 -2.2713213 0.06327871
|
||||
64000 17.54594 -1.3592836 0.9694558 4.1363258 4.3547729 -2.3818433 0.12634448
|
||||
65000 16.962312 -0.54192775 0.90321315 4.0788618 4.2008255 -2.1376711 0.039504515
|
||||
66000 18.078619 -1.3552947 1.0716861 3.3285374 4.7229362 -2.3331115 0.21978698
|
||||
67000 17.132732 -1.4376876 0.91486534 4.4461852 4.6894176 -2.3655045 0.068150385
|
||||
68000 18.69286 -1.2856207 0.3895394 3.0620063 4.9922992 -2.3459189 0.079879643
|
||||
69000 18.329552 -1.1545957 0.88632275 3.1741058 4.4562418 -2.7094867 0.25329613
|
||||
70000 16.681168 -0.94434373 1.2450393 4.5737944 4.4902996 -2.4581775 0.15313095
|
||||
71000 17.375032 -1.0514442 1.0741595 3.4896146 4.8407713 -2.5302576 0.13640847
|
||||
72000 17.833013 -0.9047134 0.87067876 3.1658924 4.8825932 -2.4398117 0.2343991
|
||||
73000 17.421411 -1.2190741 0.73706811 4.2895 4.6464636 -2.3872727 0.19696525
|
||||
74000 17.383158 -0.34208984 0.71333984 3.2718891 4.2718495 -2.2484281 0.10827022
|
||||
75000 17.20885 -1.2710479 1.125102 3.8414467 5.3222741 -2.375505 0.12910797
|
||||
76000 16.811578 -0.545162 0.59076961 3.9118604 4.8031296 -2.2777895 0.063015508
|
||||
77000 16.679231 -0.080955983 0.7253398 3.4203454 5.0987608 -2.379614 0.12961874
|
||||
78000 18.164524 -1.3115525 0.92526408 3.5764487 4.3814882 -2.3712488 0.073436724
|
||||
79000 17.738686 -1.0697859 1.2186866 3.0593848 4.6551053 -2.2505871 0.075340661
|
||||
80000 16.767483 -0.84777477 1.03128 4.1982958 4.6992227 -2.4146425 0.079774219
|
||||
81000 16.257265 0.62803774 0.84032194 3.3873471 5.0961071 -2.7219776 0.20467848
|
||||
82000 18.232082 -1.2129302 0.50746051 3.9207128 4.5073437 -2.599371 0.094522372
|
||||
83000 16.618985 -0.60917055 0.8825847 3.805497 4.9560959 -2.2194726 0.14852687
|
||||
84000 17.90762 -0.82336075 0.90504161 3.0324198 4.7444271 -2.5036073 0.15860682
|
||||
85000 16.699883 -0.50297228 0.83405307 3.8598996 4.7971968 -2.2427788 0.10338668
|
||||
86000 16.353038 -0.0096880616 0.80705167 4.0865115 4.5364338 -2.4548873 0.098456203
|
||||
87000 17.887331 -0.75281219 1.0030148 4.0117123 4.3443074 -2.9774392 0.16190152
|
||||
88000 18.583708 -1.4867053 0.86324814 3.3971237 4.3526221 -2.221239 0.14459352
|
||||
89000 17.684828 -1.283764 1.0021118 3.5426808 4.9057005 -2.3921967 0.05844702
|
||||
90000 17.2597 -0.84306489 0.99797936 3.8896866 4.4315457 -2.5662899 0.18270206
|
||||
91000 16.705581 -0.44704047 0.75239556 3.470805 4.976868 -2.1894571 0.12312848
|
||||
92000 17.548071 -1.2222664 0.92898812 4.0813773 4.3432647 -2.1631158 0.14071343
|
||||
93000 17.163675 -0.94994776 0.96876981 3.9137692 4.4388666 -2.1260232 0.13187968
|
||||
94000 18.842071 -1.2822113 0.58767049 3.1393475 4.5820965 -2.7264682 0.10406266
|
||||
95000 18.112287 -1.1011381 0.63546648 3.4672667 4.486275 -2.2991936 0.041589685
|
||||
96000 17.102713 -0.6877313 0.8389032 3.6892719 4.5676004 -2.1905327 0.13507011
|
||||
97000 16.778253 -1.2902153 1.1588744 4.2820083 4.9537657 -2.4798159 0.35696636
|
||||
98000 18.34638 -1.2908146 1.185356 3.0739807 4.4575453 -2.3959144 0.22407922
|
||||
99000 17.995148 -1.3939639 0.7727299 3.8774144 4.4345458 -2.1142776 0.13550099
|
||||
100000 18.444746 -1.2456693 0.86061526 3.468696 4.5264336 -2.4239851 0.074369539
|
||||
Loop time of 2.52011 on 4 procs for 100000 steps with 34 atoms
|
||||
|
||||
Performance: 6856.851 ns/day, 0.004 hours/ns, 39680.850 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.072506 | 0.28131 | 0.69088 | 46.2 | 11.16
|
||||
Bond | 0.050544 | 0.45307 | 0.9416 | 57.6 | 17.98
|
||||
Neigh | 0.0060885 | 0.0061619 | 0.0062056 | 0.1 | 0.24
|
||||
Comm | 0.44686 | 1.3679 | 2.0111 | 53.5 | 54.28
|
||||
Output | 0.0028057 | 0.0029956 | 0.003264 | 0.3 | 0.12
|
||||
Modify | 0.028202 | 0.095174 | 0.15782 | 19.8 | 3.78
|
||||
Other | | 0.3135 | | | 12.44
|
||||
|
||||
Nlocal: 8.5 ave 14 max 2 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 25.5 ave 32 max 20 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 98.75 ave 242 max 31 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 = 246
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,207 @@
|
|||
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
|
||||
|
|
@ -0,0 +1,207 @@
|
|||
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 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
|
||||
Loading…
Reference in New Issue