[gmx-users] core dumped during equilibration in gromacs
ISHRAT JAHAN
jishrat17 at gmail.com
Tue Apr 18 06:52:29 CEST 2017
Dear all,
I am trying to simulate protein in urea box using "amber99sb-ildn" force
field.During the equilibration following error occur-Step 8, time 0.016
(ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000027, max 0.000527 (between atoms 2089 and 2094)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 32.3 0.1010 0.1010 0.1010
Step 9, time 0.018 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000045, max 0.001791 (between atoms 2094 and 2096)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 31.6 0.1010 0.1008 0.1010
Step 10, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000042, max 0.001334 (between atoms 2094 and 2096)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 31.4 0.1008 0.1009 0.1010
Step 11, time 0.022 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000414, max 0.019232 (between atoms 2211 and 2213)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 31.8 0.1009 0.1010 0.1010
2211 2213 89.9 0.1010 0.1029 0.1010
Step 12, time 0.024 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.019085, max 0.929098 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 31.7 0.1010 0.1011 0.1010
2211 2213 80.4 0.1029 0.1011 0.1010
2334 2336 34.5 0.1010 0.1010 0.1010
2390 2392 90.0 0.1010 0.1948 0.1010
Back Off! I just backed up step12b.pdb to ./#step12b.pdb.5#
Back Off! I just backed up step12c.pdb to ./#step12c.pdb.5#
Wrote pdb files with previous and current coordinates
Step 13, time 0.026 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006403, max 0.311412 (between atoms 2251 and 2253)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 30.3 0.1011 0.1011 0.1010
2211 2213 89.9 0.1011 0.1018 0.1010
2251 2253 90.0 0.1010 0.1325 0.1010
2334 2336 33.1 0.1010 0.1008 0.1010
2390 2392 83.1 0.1948 0.1014 0.1010
Step 14, time 0.028 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022359, max 1.088377 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 30.3 0.1011 0.1010 0.1010
2211 2213 90.0 0.1018 0.1025 0.1010
2251 2253 79.0 0.1325 0.1012 0.1010
2334 2336 31.7 0.1008 0.1009 0.1010
2390 2392 90.0 0.1014 0.2109 0.1010
Back Off! I just backed up step14b.pdb to ./#step14b.pdb.3#
Back Off! I just backed up step14c.pdb to ./#step14c.pdb.3#
Wrote pdb files with previous and current coordinates
Step 15, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004396, max 0.211385 (between atoms 2251 and 2253)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 30.8 0.1010 0.1009 0.1010
2211 2213 56.5 0.1025 0.1010 0.1010
2251 2253 90.0 0.1012 0.1223 0.1010
2334 2336 30.8 0.1009 0.1011 0.1010
2390 2392 90.0 0.2109 0.1041 0.1010
Step 16, time 0.032 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022002, max 1.071041 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 32.0 0.1009 0.1009 0.1010
2211 2213 56.4 0.1010 0.1003 0.1010
2251 2253 90.0 0.1223 0.1015 0.1010
2334 2336 30.7 0.1011 0.1011 0.1010
2390 2392 89.9 0.1041 0.2092 0.1010
Back Off! I just backed up step16b.pdb to ./#step16b.pdb.3#
Back Off! I just backed up step16c.pdb to ./#step16c.pdb.3#
Wrote pdb files with previous and current coordinates
Step 17, time 0.034 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003338, max 0.147245 (between atoms 2251 and 2253)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 33.3 0.1009 0.1011 0.1010
2158 2160 35.6 0.1010 0.1010 0.1010
2211 2213 56.4 0.1003 0.1015 0.1010
2251 2253 89.9 0.1015 0.1159 0.1010
2334 2336 33.4 0.1011 0.1010 0.1010
2390 2392 90.0 0.2092 0.1079 0.1010
Step 18, time 0.036 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.020801, max 1.012618 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 34.4 0.1011 0.1012 0.1010
2158 2160 36.6 0.1010 0.1007 0.1010
2211 2213 53.9 0.1015 0.1012 0.1010
2251 2253 84.3 0.1159 0.1012 0.1010
2334 2336 34.5 0.1010 0.1009 0.1010
2390 2392 90.0 0.1079 0.2033 0.1010
Back Off! I just backed up step18b.pdb to ./#step18b.pdb.3#
Back Off! I just backed up step18c.pdb to ./#step18c.pdb.3#
Wrote pdb files with previous and current coordinates
Step 19, time 0.038 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005936, max 0.245155 (between atoms 2126 and 2127)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 31.3 0.1012 0.1011 0.1010
2126 2127 90.0 0.1010 0.1258 0.1010
2158 2160 37.3 0.1007 0.1009 0.1010
2211 2213 52.9 0.1012 0.1004 0.1010
2251 2253 90.0 0.1012 0.1021 0.1010
2334 2336 35.3 0.1009 0.1009 0.1010
2390 2392 90.0 0.2033 0.1163 0.1010
Step 20, time 0.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.019567, max 0.952451 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 32.1 0.1011 0.1009 0.1010
2126 2127 75.9 0.1258 0.1010 0.1010
2158 2160 38.0 0.1009 0.1013 0.1010
2211 2213 56.5 0.1004 0.1012 0.1010
2251 2253 90.0 0.1021 0.1023 0.1010
2334 2336 35.9 0.1009 0.1011 0.1010
2390 2392 89.9 0.1163 0.1972 0.1010
Back Off! I just backed up step20b.pdb to ./#step20b.pdb.3#
Back Off! I just backed up step20c.pdb to ./#step20c.pdb.3#
Wrote pdb files with previous and current coordinates
Step 21, time 0.042 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002521, max 0.116842 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 30.2 0.1009 0.1009 0.1010
2123 2124 37.8 0.1010 0.1006 0.1010
2126 2127 90.1 0.1010 0.1046 0.1010
2158 2160 40.4 0.1013 0.1013 0.1010
2211 2213 54.5 0.1012 0.1016 0.1010
2251 2253 64.2 0.1023 0.1009 0.1010
2334 2336 34.9 0.1011 0.1013 0.1010
2390 2392 90.1 0.1972 0.1128 0.1010
Step 22, time 0.044 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018059, max 0.878624 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 30.6 0.1009 0.1009 0.1010
2123 2124 36.1 0.1006 0.1004 0.1010
2126 2127 90.0 0.1046 0.1037 0.1010
2158 2160 39.7 0.1013 0.1007 0.1010
2211 2213 53.5 0.1016 0.1003 0.1010
2251 2253 62.7 0.1009 0.1002 0.1010
2334 2336 38.4 0.1013 0.1011 0.1010
2390 2392 90.0 0.1128 0.1897 0.1010
Back Off! I just backed up step22b.pdb to ./#step22b.pdb.3#
Back Off! I just backed up step22c.pdb to ./#step22c.pdb.3#
Wrote pdb files with previous and current coordinates
Step 23, time 0.046 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005118, max 0.236688 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 30.6 0.1009 0.1010 0.1010
2123 2124 31.2 0.1004 0.0995 0.1010
2126 2127 89.9 0.1037 0.1086 0.1010
2158 2160 38.4 0.1007 0.1008 0.1010
2211 2213 53.5 0.1003 0.1008 0.1010
2251 2253 62.0 0.1002 0.1019 0.1010
2334 2336 37.4 0.1011 0.1007 0.1010
2390 2392 90.0 0.1897 0.1249 0.1010
Step 24, time 0.048 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.016837, max 0.819486 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2126 2127 90.0 0.1086 0.1023 0.1010
2158 2160 37.8 0.1008 0.1010 0.1010
2211 2213 52.8 0.1008 0.1016 0.1010
2251 2253 58.7 0.1019 0.1007 0.1010
2334 2336 36.2 0.1007 0.1008 0.1010
2390 2392 90.0 0.1249 0.1838 0.1010
Back Off! I just backed up step24b.pdb to ./#step24b.pdb.3#
Back Off! I just backed up step24c.pdb to ./#step24c.pdb.3#
Wrote pdb files with previous and current coordinates
Step 25, time 0.05 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005570, max 0.256892 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2126 2127 89.9 0.1023 0.1097 0.1010
2158 2160 36.9 0.1010 0.1011 0.1010
2211 2213 54.9 0.1016 0.1009 0.1010
2251 2253 60.8 0.1007 0.1004 0.1010
2334 2336 34.9 0.1008 0.1011 0.1010
2390 2392 90.0 0.1838 0.1269 0.1010
Step 26, time 0.052 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.014557, max 0.706394 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2126 2127 90.0 0.1097 0.1065 0.1010
2158 2160 36.3 0.1011 0.1010 0.1010
2211 2213 55.9 0.1009 0.1003 0.1010
2251 2253 64.3 0.1004 0.1021 0.1010
2334 2336 34.1 0.1011 0.1012 0.1010
2390 2392 90.0 0.1269 0.1723 0.1010
Back Off! I just backed up step26b.pdb to ./#step26b.pdb.3#
Back Off! I just backed up step26c.pdb to ./#step26c.pdb.3#
Wrote pdb files with previous and current coordinates
Step 27, time 0.054 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006686, max 0.319495 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2126 2127 89.9 0.1065 0.1072 0.1010
2158 2160 37.6 0.1010 0.1008 0.1010
2211 2213 58.5 0.1003 0.1017 0.1010
2251 2253 62.7 0.1021 0.1004 0.1010
2334 2336 31.8 0.1012 0.1010 0.1010
2390 2392 90.1 0.1723 0.1333 0.1010
Step 28, time 0.056 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.013884, max 0.675418 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2126 2127 90.0 0.1072 0.1035 0.1010
2158 2160 38.2 0.1008 0.1008 0.1010
2211 2213 48.9 0.1017 0.1011 0.1010
2251 2253 62.0 0.1004 0.1007 0.1010
2334 2336 31.3 0.1010 0.1009 0.1010
2390 2392 90.0 0.1333 0.1692 0.1010
Back Off! I just backed up step28b.pdb to ./#step28b.pdb.3#
Back Off! I just backed up step28c.pdb to ./#step28c.pdb.3#
Wrote pdb files with previous and current coordinates
Step 29, time 0.058 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006736, max 0.312627 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 30.4 0.1010 0.1011 0.1010
2126 2127 90.0 0.1035 0.1109 0.1010
2158 2160 39.4 0.1008 0.1012 0.1010
2211 2213 48.1 0.1011 0.1004 0.1010
2251 2253 60.3 0.1007 0.1019 0.1010
2334 2336 32.5 0.1009 0.1010 0.1010
2390 2392 90.3 0.1692 0.1326 0.1010
Step 30, time 0.06 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009507, max 0.458278 (between atoms 2387 and 2389)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2094 2096 30.2 0.1011 0.1011 0.1010
2123 2124 30.8 0.1007 0.1013 0.1010
2126 2127 90.0 0.1109 0.1070 0.1010
2158 2160 40.4 0.1012 0.1014 0.1010
2211 2213 47.9 0.1004 0.1010 0.1010
2251 2253 57.3 0.1019 0.1004 0.1010
2334 2336 33.8 0.1010 0.1012 0.1010
2387 2388 30.2 0.1011 0.1025 0.1010
2387 2389 90.2 0.1012 0.1473 0.1010
2390 2392 76.0 0.1326 0.1012 0.1010
Step 31, time 0.062 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005728, max 0.277854 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2126 2127 90.0 0.1070 0.1020 0.1010
2158 2160 31.5 0.1014 0.1010 0.1010
2211 2213 43.7 0.1010 0.1013 0.1010
2251 2253 55.2 0.1004 0.1007 0.1010
2334 2336 32.9 0.1012 0.1012 0.1010
2387 2389 44.9 0.1473 0.1003 0.1010
2390 2392 90.2 0.1012 0.1291 0.1010
Step 32, time 0.064 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001969, max 0.073065 (between atoms 2387 and 2389)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2123 2124 37.5 0.1012 0.1010 0.1010
2126 2127 90.0 0.1020 0.1057 0.1010
2158 2160 31.2 0.1010 0.1009 0.1010
2211 2213 42.7 0.1013 0.1009 0.1010
2251 2253 57.7 0.1007 0.1020 0.1010
2334 2336 30.5 0.1012 0.1010 0.1010
2387 2389 90.5 0.1003 0.1084 0.1010
2390 2392 86.4 0.1291 0.1015 0.1010
Step 33, time 0.066 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006294, max 0.304247 (between atoms 2390 and 2392)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2123 2124 35.7 0.1010 0.1008 0.1010
2126 2127 85.7 0.1057 0.1002 0.1010
2158 2160 30.7 0.1009 0.1008 0.1010
2190 2191 33.3 0.1011 0.1011 0.1010
2211 2213 44.1 0.1009 0.1007 0.1010
2251 2253 58.7 0.1020 0.1004 0.1010
2334 2336 30.3 0.1010 0.1008 0.1010
2387 2389 76.9 0.1084 0.0993 0.1010
2390 2392 89.9 0.1015 0.1317 0.1010
Step 34, time 0.068 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 133.867793, max 4615.651855 (between atoms 2387 and 2389)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2035 2037 48.7 0.1010 0.1010 0.1010
2123 2124 35.1 0.1008 0.1008 0.1010
2126 2127 90.0 0.1002 0.1088 0.1010
2190 2191 30.6 0.1011 0.1009 0.1010
2211 2213 45.7 0.1007 0.1010 0.1010
2251 2253 58.1 0.1004 0.1005 0.1010
2385 2386 56.8 0.1213 0.0892 0.1229
2385 2387 99.7 0.1317 0.2141 0.1335
2385 2390 97.5 0.1316 0.3057 0.1335
2387 2388 94.8 0.1012 0.2607 0.1010
2387 2389 88.7 0.0993 466.2818 0.1010
2390 2391 85.9 0.1029 0.2297 0.1010
2390 2392 119.4 0.1317 464.7838 0.1010
Back Off! I just backed up step34b.pdb to ./#step34b.pdb.3#
Back Off! I just backed up step34c.pdb to ./#step34c.pdb.3#
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
Please help me in solving above problem.
Thanks in advance.
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