Haven't had a chance to reproduce as I don't take periodic backups on this machine
EDIT: ok, I could do that if I undeleted relevant queue entry (too lazy to do that just yet)
Log excerpt follows (full log available upon request).
Code: Select all
[05:06:50] Completed 175000 out of 250000 steps (70%)
[05:14:42] Completed 177500 out of 250000 steps (71%)
[05:22:34] Completed 180000 out of 250000 steps (72%)
[05:30:27] Completed 182500 out of 250000 steps (73%)
Step 27432900, time 54865.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.360012, max 18.521997 (between atoms 7103 and 7104)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7100 7102 90.0 0.1090 1.9903 0.1090
Warning: 1-4 interaction between 7102 and 7104 at distance 3.926 which is larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 27432901, time 54865.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.036675, max 2.022461 (between atoms 22784 and 22785)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22784 22785 90.0 0.1080 0.3264 0.1080
Step 27432901, time 54865.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 4409648120517.936523, max 291538319966208.000000 (between atoms 7100 and 7102)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22232 22233 90.0 0.1090 1.8879 0.1090
22239 22240 90.2 0.1090 2274.1292 0.1090
22239 22241 90.1 0.1090 2566.5967 0.1090
22239 22242 90.0 0.1090 23362.0273 0.1090
22289 22290 90.0 0.1090 4.8147 0.1090
22292 22294 90.0 0.1090 1389668736.0000 0.1090
22295 22296 90.0 0.1090 6.3375 0.1090
22298 22299 90.0 0.1010 48893708.0000 0.1010
7029 7030 90.0 0.1090 147.3939 0.1090
7031 7032 90.0 0.1090 1.8789 0.1090
7031 7033 90.0 0.1090 0.6695 0.1090
22784 22785 90.0 0.1080 0.3264 0.1080
7100 7101 90.0 0.1158 4885670526976.0000 0.1090
7100 7102 90.0 1.9903 31777676591104.0000 0.1090
7103 7105 90.0 0.1007 1009561763840.0000 0.1010
7103 7106 90.0 0.0981 806190579712.0000 0.1010
7250 7251 90.0 0.0960 49772952.0000 0.0960
7081 7084 90.0 0.1090 52815224832.0000 0.1090
7055 7057 90.0 0.1090 4303412.5000 0.1090
7065 7066 90.0 0.1090 22171224.0000 0.1090
7133 7135 90.0 0.1090 0.1205 0.1090
7202 7203 90.0 0.1010 29740.4414 0.1010
7204 7205 90.0 0.1090 1272635392.0000 0.1090
7239 7240 90.0 0.1090 2.2167 0.1090
7241 7243 90.0 0.1090 4.7556 0.1090
7245 7246 90.0 0.1080 11248352.0000 0.1080
7237 7238 90.0 0.1010 208.3328 0.1010
t = 54865.805 ps: Water molecule starting at atom 113161 can not be settled.
Check for bad contacts and/or reduce the timestep.
[0]0:Return code = 0, signaled with Segmentation fault
[0]1:Return code = 0, signaled with Segmentation fault
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 0, signaled with Quit
[05:31:47] CoreStatus = 0 (0)tear
That's the one!