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