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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