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Hi
I am trying to run md with nvt conditions (after making a box, adding solvent and ions).
and this error comes up:
Using 1 MPI process
Using 112 OpenMP threads
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005329, max 0.040149 (between atoms 32 and 33)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
starting mdrun ‘Protein in water’
25000 steps, 50.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 12.364191, max 103.412048 (between atoms 32 and 34)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
45 46 45.2 0.1015 0.1432 0.1010
45 47 32.2 0.1459 0.1826 0.1449
43 44 80.4 0.1243 0.2518 0.1229
43 45 81.7 0.1356 0.2820 0.1335
35 36 146.6 0.1106 4.8013 0.1090
35 37 154.9 0.1097 5.0728 0.1090
32 33 129.1 0.1134 9.9818 0.1090
32 34 157.6 0.1125 11.3809 0.1090
15 17 35.8 0.1344 0.1857 0.1335
27 28 66.9 0.1101 0.1586 0.1090
27 29 61.9 0.1537 0.3394 0.1522
17 18 35.0 0.1454 0.1873 0.1449
17 27 76.5 0.1464 0.3063 0.1449
21 24 43.9 0.1528 0.2142 0.1526
41 42 84.4 0.1078 0.6407 0.1090
41 43 78.1 0.1559 0.6982 0.1522
38 39 82.9 0.1107 0.5383 0.1090
38 40 72.1 0.1105 0.2465 0.1090
38 41 83.4 0.1545 0.8577 0.1526
31 32 63.4 0.1466 9.6456 0.1449
125 126 94.3 0.1016 0.7553 0.1010
125 127 93.2 0.1016 0.8601 0.1010
123 124 43.2 0.1235 5.5592 0.1229
123 125 77.3 0.1335 0.3103 0.1335
120 121 102.8 0.1098 0.3169 0.1090
120 122 97.8 0.1097 0.3367 0.1090
120 123 84.0 0.1524 1.1513 0.1522
118 120 125.6 0.1540 0.2429 0.1526
29 30 68.5 0.1246 0.3886 0.1229
24 25 52.6 0.1093 0.1819 0.1090
24 26 49.5 0.1092 0.1729 0.1090
24 27 80.8 0.1538 0.3126 0.1526
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
Why? IT WORKS FINE when I do the same peptide with a different starting conformation.
Best,
Miriam