[gmx-users] crashed run
Justin A. Lemkul
jalemkul at vt.edu
Thu Dec 9 16:02:39 CET 2010
shiva birgani wrote:
>
> 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?
Please provide the exact commands you used to continue your run and carry out
your RMSD analysis. Without that precise information, the best guess is "you
did something wrong."
You probably used the wrong .tpr file as your reference structure. It seems odd
to me that your t=0 RMSD is so high.
-Justin
> 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
> .
> .
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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