[gmx-users] gromacs doubt
manjula kasinathan
manjubfs at gmail.com
Sat May 8 12:40:43 CEST 2010
hi all
i'm doing simulation for complex structure (protein length around
1020). while running mdrun for position restrain it shows error like this
Step 434, time 0.868 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1818.708939, max 108974.859375 (between atoms 1917 and 1918)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2873 2875 90.0 0.1503 0.1088 0.1000
1930 1932 66.8 0.1764 0.2060 0.1470
1930 1931 69.3 0.1413 0.2511 0.1000
1925 1927 33.2 0.1241 0.1563 0.1250
1925 1926 54.0 0.1238 0.1773 0.1250
1924 1925 50.0 0.1514 4.6004 0.1530
1923 1924 156.4 0.2264 20.8825 0.1530
1921 1923 139.8 0.2458 45.8946 0.1470
1921 1922 116.5 0.1880 34.8778 0.1000
1919 1920 42.5 0.2799 206.5039 0.1230
1917 1919 83.9 0.3952 1749.0353 0.1530
1917 1918 90.2 0.7744 16673.3066 0.1530
1915 1917 96.0 0.5866 1624.9022 0.1470
1915 1916 93.7 0.2045 470.1029 0.1000
1913 1915 88.9 0.3074 522.5389 0.1330
1913 1914 115.2 0.3731 11.2578 0.1230
1912 1913 117.0 0.1173 11.5079 0.1530
1910 1912 91.5 0.1471 80.4026 0.1470
1910 1911 128.1 0.1822 34.9078 0.1000
1908 1910 90.1 0.1345 6296.6333 0.1330
1908 1909 89.0 0.1590 6080.4458 0.1230
1905 1906 90.2 0.0989 642.7140 0.1000
1904 1907 90.0 0.1530 7623.7417 0.1530
1904 1905 90.0 0.1416 7605.1113 0.1430
1903 1908 89.3 0.1776 7638.7241 0.1530
1903 1904 90.0 0.1665 4890.0454 0.1530
1901 1903 91.3 0.1556 8921.3604 0.1470
1901 1902 65.9 0.1047 59.7358 0.1000
1899 1900 176.1 0.1212 121.1425 0.1230
1894 1899 34.3 0.1521 87.4365 0.1530
1894 1895 90.5 0.1513 11.8270 0.1530
1892 1894 107.0 0.1453 12.1096 0.1470
1892 1893 76.7 0.0988 1.3052 0.1000
1890 1892 49.3 0.1318 1.3995 0.1330
1890 1891 57.8 0.1215 0.0482 0.1230
1886 1890 34.4 0.1511 0.0948 0.1530
1437 1438 69.2 0.0989 0.2078 0.1000
1436 1437 89.7 0.1345 0.2161 0.1360
1434 1436 62.0 0.1375 0.0617 0.1390
1434 1435 39.0 0.1078 0.1438 0.1090
1432 1436 91.0 0.1375 2.8230 0.1390
1432 1433 90.7 0.1078 1.1621 0.1090
1430 1434 102.3 0.1375 0.2004 0.1390
1430 1431 94.7 0.1078 0.1235 0.1090
1428 1432 89.2 0.1375 2.1372 0.1390
1428 1429 91.2 0.1078 1.6125 0.1090
1427 1430 87.0 0.1375 0.9626 0.1390
1427 1428 92.1 0.1375 1.8618 0.1390
1426 1427 93.3 0.1514 0.8468 0.1530
8326 8328 89.9 0.4409 1.1304 0.1000
8326 8327 90.1 0.4916 0.2944 0.1000
8324 8326 90.3 0.1156 0.2084 0.1330
8324 8325 88.6 0.1134 0.1387 0.1230
8323 8324 48.0 0.1226 0.2008 0.1530
8322 8323 31.2 0.1656 0.1504 0.1530
8320 8321 38.4 0.1375 0.0957 0.1000
8091 8092 38.4 0.0991 0.1000 0.1000
8001 8002 90.0 0.0982 0.1635 0.1000
7838 7840 90.1 0.1018 0.1239 0.1000
6599 6600 38.1 0.0990 0.1002 0.1000
5583 5585 89.9 0.0983 0.1465 0.1000
5524 5525 38.7 0.0992 0.1004 0.1000
t = 0.868 ps: Water molecule starting at atom 36658 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
wat should i do.i carried out mdrun for 10ps nsteps=5000. can any one help
me to overcome this error. thanks in advance.
--
With Regards,
Manjulakasinathan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100508/6c036798/attachment.html>
More information about the gromacs.org_gmx-users
mailing list