[gmx-users] crashed run

[shiva birgani]

Dear friends
Thanks for help
I did what you said. but now I have another question.
why when I compute RMSD, there is a turbulence in the digits  between two MD
runs (MD1 & MD2)?
Along 10nS RMSD values increase but after that in continued MD RMSD values
start with lower digits. So the obtained RMSD plot has turbulence in the gap
between two MD.
how can I solve this problem?
to clear this question I put the RMSD values of some frames below:

   0.0000000    0.2210472
   0.0100000    0.2029170
   0.0200000    0.2312521
   0.0300000    0.2153534
   0.0400000    0.2236744
   0.0500000    0.2186773
   0.0600000    0.2058581
   0.0700000    0.2236195
   0.0800000    0.2124665
   0.0900000    0.1984987
   0.1000000    0.2133160
   0.1100000    0.2032684
   0.1200000    0.2185176
   0.1300000    0.2375279
   0.1400000    0.2209899
   0.1500000    0.2517494
   0.1600000    0.2250047
   0.1700000    0.2311087
   0.1800000    0.2404595
   0.1900000    0.2289306
   0.2000000    0.2239618
   .
   .
   .
   5.0000000    0.1890597
   5.0100002    0.1890515
   5.0200005    0.2006893
   5.0300002    0.1972803
   5.0400004    0.1982047
   5.0500002    0.1675302
   5.0600004    0.1850004
   5.0700002    0.1860897
   5.0800004    0.2052469
   5.0900002    0.1921552
   5.1000004    0.2011560
   5.1100001    0.1885858
   5.1200004    0.2002560
   5.1300001    0.1740426
   5.1400003    0.1723358
   5.1500006    0.1674020
   5.1600008    0.1726498
   5.1700006    0.1708745
   5.1800008    0.1729662
   5.1900005    0.1796937
   5.2000008    0.1865102
   .
   .
   9.0000000    0.1759290
   9.0100002    0.1719585
   9.0200005    0.1677127
   9.0300007    0.1568936
   9.0400000    0.1683941
   9.0500002    0.1726477
   9.0600004    0.1535644
   9.0700006    0.1613303
   9.0800009    0.1731772
   9.0900002    0.1845323
   9.1000004    0.1906714
   9.1100006    0.1809433
   9.1200008    0.1692949
   9.1300001    0.1600803
   9.1400003    0.1660035
   9.1500006    0.1754447
   9.1600008    0.1643370
   9.1700001    0.1781539
   9.1800003    0.1826023
   9.1900005    0.1772111
   9.2000008    0.1583686
   .
   .
  10.0000000    0.0005027 -----------------------here MD1 crashed and new
MD2 started
  10.0100002    0.0855930
  10.0200005    0.0906140
  10.0300007    0.1090365
  10.0400009    0.1284636
  10.0500002    0.1079870
  10.0600004    0.1182096
  10.0700006    0.1337083
  10.0800009    0.1404199
  10.0900002    0.1518639
  10.1000004    0.1318038
  10.1100006    0.1288120
  10.1200008    0.1413255
  10.1300001    0.1318252
  10.1400003    0.1459130
  10.1500006    0.1559724
  10.1600008    0.1299423
  10.1700001    0.1178040
  10.1800003    0.1542594
  10.1900005    0.1464352
  10.2000008    0.1217079
  .
  .
  15.0000019    0.3443058
  15.0100021    0.3503898
  15.0200014    0.3517708
  15.0300016    0.3573279
  15.0400019    0.3375081
  15.0500021    0.3556643
  15.0600014    0.3347272
  15.0700016    0.3550032
  15.0800018    0.3570938
  15.0900021    0.3791857
  15.1000013    0.3838716
  15.1100016    0.3931288
  15.1200018    0.3871831
  15.1300020    0.3749425
  15.1400013    0.3714155
  15.1500015    0.3525784
  15.1600018    0.3199620
  15.1700020    0.3337676
  15.1800013    0.3514860
  15.1900015    0.3480204
  15.2000017    0.3494628
  .
  .
  20.0000000    0.3118807
  20.0100002    0.3075790
  20.0200005    0.3048350
  20.0300007    0.3090370
  20.0400009    0.3213491
  20.0500011    0.3106411
  20.0600014    0.2958525
  20.0700016    0.2954315
  20.0800018    0.2988622
  20.0900002    0.2828163
  20.1000004    0.3012785
  20.1100006    0.2912732
  20.1200008    0.3035305
  20.1300011    0.3047263
  20.1400013    0.2943486
  20.1500015    0.2992145
  20.1600018    0.3017998
  20.1700001    0.3055096
  20.1800003    0.3006694
  20.1900005    0.2961275
  20.2000008    0.2953818
  .
  .
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