The breaking molecule

Hi,
I want to calculate C_26H_54.
If I run the following script,I get a message 'ERROR: Lost atoms:
original 80 current 76 (thermo.cpp:385)'.
I think that the molecule has broken.
The place where input is bad does not find somewhere.
Plz,give me advice about my input (and data.*).

Thanks,

input is following ...

# ---------- Initialize Simulation ---------------------
clear
units real
dimension 3
newton on
boundary f f f
atom_style atomic

# ---------- Read data ---------------------
read_data data.poly

#----------- Setting-------------------------
#mass 1 1.00080
#mass 2 12.0110
pair_style airebo 3.0 0 0
pair_coeff * * ../../../potentials/CH.airebo C H

# Equilibration

velocity all create 200.0 1247 rot yes mom yes

fix 1 all nve

timestep 0.1

dump 1 all custom 100 dump.comp.*.lammpstrj id type x y z
vx vy vz fx fy fz

run 1000

Hi,
I want to calculate C_26H_54.
If I run the following script,I get a message 'ERROR: Lost atoms:
original 80 current 76 (thermo.cpp:385)'.
I think that the molecule has broken.
The place where input is bad does not find somewhere.

there is already a mistake with the second command.
you are using AIREBO, but have set to use "real" units.
this is wrong. AIREBO *requires* to use "metal" units.
please read the documentation more carefully.

axel.

Thank you for your reply.
The problem was solved.
I appreciate.
Is preservation of Total energies of output OK?
It saves to the first decimal place.
Thank you.

# ---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
newton on
boundary f f f
atom_style atomic

# ---------- Read data ---------------------
read_data data.poly

#----------- Setting-------------------------
#mass 1 1.00080
#mass 2 12.0110
pair_style airebo 3.0 0 0
pair_coeff * * ../../../potentials/CH.airebo H C

# Equilibration

velocity all create 200.0 1247 rot yes mom yes

fix 1 all nve

thermo 1
timestep 0.001

dump 1 all custom 100 dump.comp.*.lammpstrj id type x y z
vx vy vz fx fy fz

run 1000

output

Reading data file ...
  orthogonal box = (-50 -50 -50) to (50 50 50)
  2 by 2 by 2 MPI processor grid
  80 atoms
start
Setting up run ...
Memory usage per processor = 0.859539 Mbytes
Step Temp E_pair E_mol TotEng Press
       0 200 -336.17269 0 -334.13038 25.179909
       1 188.98588 -336.04908 0 -334.11924 21.653797
       2 153.8269 -335.67271 0 -334.1019 13.788722
       3 116.54568 -335.284 0 -334.09389 3.9306521
       4 90.050887 -335.00947 0 -334.08992 -4.9685014
       5 80.439199 -334.90839 0 -334.08698 -10.305153
       6 89.876204 -335.01064 0 -334.09286 -10.29942
       7 109.41923 -335.22167 0 -334.10433 -3.7575063
       8 127.60458 -335.40476 0 -334.10172 6.6183999
       9 148.33825 -335.61411 0 -334.09935 15.379147
      10 168.95736 -335.84739 0 -334.12207 18.322398
      11 163.67192 -335.78739 0 -334.11605 24.12401
      12 140.25008 -335.52089 0 -334.08872 24.766625
      13 125.03049 -335.38029 0 -334.10354 13.857817
      14 111.68514 -335.22655 0 -334.08607 1.9377394
      15 102.81187 -335.13207 0 -334.08221 -5.7859197
      16 108.61491 -335.19187 0 -334.08275 -10.151076
      17 127.61847 -335.39398 0 -334.0908 -10.038361
      18 148.56526 -335.61914 0 -334.10206 -5.523312
      19 156.21022 -335.70246 0 -334.10732 2.0667793
      20 144.72183 -335.57681 0 -334.09897 10.695778
      21 127.20149 -335.38604 0 -334.08712 17.022224
      22 116.93941 -335.28743 0 -334.0933 19.62993
      23 114.35892 -335.2617 0 -334.09392 17.817261
      24 117.5857 -335.29804 0 -334.0973 9.9539165
      25 121.89751 -335.34174 0 -334.09697 -1.1299924
      26 124.68293 -335.36871 0 -334.0955 -11.040689
      27 127.70555 -335.39542 0 -334.09135 -17.087378
      28 133.85122 -335.45974 0 -334.09291 -17.882642
      29 140.29539 -335.53364 0 -334.10101 -13.158281
      30 137.39395 -335.50861 0 -334.10561 -3.2494552
      31 123.96353 -335.35834 0 -334.09248 8.3220645
      32 115.74219 -335.2693 0 -334.0874 17.096022
      33 121.61431 -335.33353 0 -334.09166 21.066972
      34 135.40892 -335.47956 0 -334.09683 20.206819
      35 146.07877 -335.59362 0 -334.10193 15.114767
      36 145.77645 -335.58908 0 -334.10048 7.7457612
      37 136.34512 -335.48795 0 -334.09565 -0.2891284
      38 124.27848 -335.35955 0 -334.09048 -6.6961584
      39 116.54107 -335.27747 0 -334.0874 -9.6400147
      40 116.46451 -335.27925 0 -334.08996 -8.2855802
      41 120.44558 -335.3247 0 -334.09477 -3.0337164
      42 120.48854 -335.33115 0 -334.10077 5.9688854
      43 119.73133 -335.31086 0 -334.08822 16.360027
      44 135.1968 -335.47768 0 -334.09711 19.512717
      45 154.80043 -335.70025 0 -334.1195 13.735051
      46 150.14889 -335.64724 0 -334.11399 9.5022103
      47 132.95112 -335.45385 0 -334.09621 3.4282231
      48 123.49342 -335.36637 0 -334.10531 -7.1629409
      49 117.21017 -335.29474 0 -334.09784 -15.370244
      50 113.79144 -335.25789 0 -334.0959 -18.385857
      51 116.22552 -335.28438 0 -334.09753 -15.863508
      52 122.59888 -335.35241 0 -334.10049 -8.7408843
      53 130.34142 -335.43042 0 -334.09943 0.88797914
      54 140.85145 -335.53643 0 -334.09812 10.524689
      55 154.95128 -335.6907 0 -334.10841 16.435622
      56 161.81155 -335.76624 0 -334.11389 17.268901
      57 152.29274 -335.66347 0 -334.10832 13.429201
      58 133.12058 -335.45693 0 -334.09756 6.020241
      59 117.49367 -335.29279 0 -334.093 -3.0009636
      60 112.08581 -335.23806 0 -334.09349 -10.853906
      61 116.33256 -335.28319 0 -334.09526 -15.284646
      62 126.47167 -335.39119 0 -334.09972 -14.939863
      63 134.88203 -335.48429 0 -334.10693 -8.7471425
      64 138.34984 -335.51098 0 -334.09822 1.1081755
      65 144.41621 -335.58318 0 -334.10847 9.345455
      66 148.27971 -335.62551 0 -334.11134 16.269293
      67 146.85133 -335.60151 0 -334.10193 21.527298
      68 148.77865 -335.63213 0 -334.11287 16.327474
      69 142.6447 -335.57385 0 -334.11723 4.042992
      70 122.18527 -335.34133 0 -334.09363 -4.6843772
      71 107.91826 -335.18942 0 -334.08741 -11.11622
      72 110.5147 -335.21946 0 -334.09094 -13.982784
      73 125.45221 -335.38176 0 -334.1007 -12.575292
      74 139.17872 -335.53062 0 -334.10939 -7.1569107
      75 140.47253 -335.54294 0 -334.1085 0.74060133
      76 131.49851 -335.43743 0 -334.09462 9.1230942
      77 129.91253 -335.41656 0 -334.08995 14.362856
      78 142.44155 -335.55669 0 -334.10214 14.073597
      79 153.16019 -335.67919 0 -334.11518 9.1138677
      80 146.19371 -335.60531 0 -334.11244 1.0671531
      81 123.69128 -335.35919 0 -334.09611 -7.9387643
      82 104.05496 -335.14736 0 -334.0848 -15.374076
      83 102.76403 -335.13458 0 -334.0852 -19.512799
      84 119.30351 -335.31359 0 -334.09532 -19.333544
      85 137.84484 -335.51786 0 -334.11025 -13.802903
      86 142.64209 -335.56498 0 -334.10838 -4.2551149
      87 138.64516 -335.51642 0 -334.10064 4.6945531
      88 138.3282 -335.50967 0 -334.09713 9.8258861
      89 144.71711 -335.58015 0 -334.10237 10.616315
      90 149.9602 -335.63947 0 -334.10815 8.3713209
      91 143.6703 -335.57632 0 -334.10922 4.1791637
      92 125.25181 -335.37886 0 -334.09985 -0.94986541
      93 107.38424 -335.18731 0 -334.09075 -6.4583581
      94 102.80481 -335.13793 0 -334.08814 -10.433881
      95 113.20342 -335.25054 0 -334.09456 -11.39105
      96 129.75138 -335.42822 0 -334.10326 -9.1310976
      97 139.43518 -335.53499 0 -334.11114 -3.7029014
      98 138.10215 -335.51455 0 -334.10431 3.0870988
      99 134.22872 -335.47466 0 -334.10398 7.9993579
     100 133.28802 -335.45995 0 -334.09887 9.4131317
     101 134.54037 -335.47941 0 -334.10555 7.0548748
     102 129.47039 -335.42351 0 -334.10142 4.0632112
     103 121.00362 -335.33249 0 -334.09686 -1.7746568
     104 114.5813 -335.27084 0 -334.10079 -10.433544
     105 109.56062 -335.21188 0 -334.09309 -16.554048
     106 110.96623 -335.22804 0 -334.0949 -19.238643
     107 117.8853 -335.30202 0 -334.09822 -17.573116
     108 125.16394 -335.3801 0 -334.10198 -12.325099
     109 127.77873 -335.40989 0 -334.10507 -4.7373996
     110 126.7693 -335.39351 0 -334.099 2.9339874
     111 128.66957 -335.41626 0 -334.10235 7.1729844
     112 132.18379 -335.45222 0 -334.10242 7.6510401
     113 133.61072 -335.46843 0 -334.10406 4.2933994
     114 130.42861 -335.43512 0 -334.10324 -2.1830601
     115 123.56673 -335.36032 0 -334.09851 -9.4283515
     116 118.90978 -335.30916 0 -334.09491 -15.785891
     117 120.74381 -335.3293 0 -334.09632 -19.314591
     118 126.84985 -335.39685 0 -334.10152 -18.916718
     119 131.04244 -335.44142 0 -334.10328 -14.5888
     120 128.9269 -335.42556 0 -334.10902 -7.3250707
     121 119.05147 -335.31056 0 -334.09486 3.0445312
     122 114.51577 -335.26632 0 -334.09694 11.195627
     123 123.83179 -335.37003 0 -334.10552 11.951639
     124 138.11343 -335.52596 0 -334.11561 5.5375288
     125 138.4601 -335.52523 0 -334.11134 -4.3208514
     126 122.25496 -335.34434 0 -334.09593 -10.999418
     127 108.9484 -335.19975 0 -334.08721 -15.390399
     128 110.85537 -335.22397 0 -334.09196 -17.35447
     129 122.66925 -335.35499 0 -334.10235 -15.591239
     130 129.66447 -335.43324 0 -334.10916 -10.398901
     131 123.05639 -335.36169 0 -334.10509 -2.9173083

Thank you for your reply.
The problem was solved.
I appreciate.
Is preservation of Total energies of output OK?

that is for *you* to decide. you cannot write in a paper
"the energy was conserved well because some random
dude on the internet said so".

axel.