[gmx-users] segmentation fault

[Magnus Andersson]

Hi all,

My constrained 20ps simulation crashes for some reason. This simulation is
very much alike other simulations I've run in a successful manner
previously. Seems like there is a probem on atoms constituting an
artificial membrane...

Anyway, I guess it is a general question. Where do you start looking if
the run crashes like this (and a slightly different system, just strctural
change, it has exactly the same atoms...)?

Error message looks like=

step 340, will finish at Tue Dec 11 12:52:51 2007
Step 344, time 0.688 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.000822 (between atoms 2262 and 2263) rms 0.000041
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2262   2263   42.4    0.1090   0.1089      0.1090
   2265   2266   30.3    0.1090   0.1090      0.1090

Step 345, time 0.69 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001312 (between atoms 2265 and 2266) rms 0.000051
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2262   2263   30.0    0.1089   0

Thankful for a reply /

Magnus Andersson