[gmx-users] Segmentation fault error during run

[Yasser Almeida Hernández]

Hi all,
I am simulating a solvated system with a membrane protein and detergent 
NG (beta-nonylgrucoside), using GROMACS 4.6.5. I got the topology for NG 
from ATB database. During the simulation I got this Segmentation fault 
error:

************
(...)
Step 173550, time 347.1 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.170158, max 8.399462 (between atoms 2306 and 2307)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
    2306   2307   90.3    0.1267   1.0527      0.1120
    2306   2308   38.0    0.1532   0.1445      0.1530
    2306   2311   80.8    0.1534   0.2344      0.1530
    2311   2312   89.4    0.1131   0.1629      0.1130
    2311   2313   86.8    0.1423   0.2395      0.1420
    2311   2315   49.1    0.1535   0.2080      0.1530
    2313   2314   52.3    0.0972   0.1227      0.0971
    2315   2316   57.5    0.1131   0.1533      0.1130
    2315   2317   50.1    0.1422   0.1846      0.1420
    2315   2319   47.7    0.1532   0.1994      0.1530
    2317   2318   37.8    0.0971   0.1220      0.0971
Wrote pdb files with previous and current coordinates

Step 173551, time 347.102 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.093200, max 4.227952 (between atoms 2306 and 2307)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
    2305   2306   53.7    0.1182   0.1114      0.1430
    2306   2307   88.0    1.0527   0.5855      0.1120
    2306   2308   64.1    0.1445   0.1706      0.1530
    2308   2309   34.5    0.1495   0.1514      0.1420
    2309   2310   40.2    0.0978   0.1113      0.0971
    2311   2312   94.2    0.1629   0.3210      0.1130
    2311   2313   75.6    0.2395   0.1580      0.1420
    2313   2314   62.0    0.1227   0.1386      0.0971
    2315   2317   59.2    0.1846   0.1394      0.1420
    2315   2319   37.0    0.1994   0.1497      0.1530
    2317   2318   35.8    0.1220   0.1015      0.0971
Wrote pdb files with previous and current coordinates

Step 173552, time 347.104 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 4885.612961, max 229375.093750 (between atoms 2317 and 2318)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
    2299   2300   31.3    0.1520   0.1785      0.1520
    2300   2301   76.4    0.1520   4.6510      0.1520
    2301   2302  142.5    0.1434  14.0997      0.1430
    2303   2304   75.3    0.1115 124.7837      0.1120
    2303   2305   82.3    0.1386 118.6994      0.1430
    2303   2319  125.8    0.1578 369.9674      0.1540
    2305   2306   83.4    0.1114  21.8297      0.1430
    2306   2307   83.9    0.5855  24.8837      0.1120
    2306   2308   72.2    0.1706  26.9393      0.1530
    2306   2311   65.9    0.1676 228.0349      0.1530
    2308   2309  143.2    0.1514   5.3767      0.1420
    2309   2310  136.9    0.1113   0.4643      0.0971
    2311   2312  123.4    0.3210 174.6479      0.1130
    2311   2313   97.1    0.1580 242.5305      0.1420
    2311   2315   83.1    0.1557 1329.8728      0.1530
    2313   2314   64.9    0.1386   4.5339      0.0971
    2315   2316   87.6    0.0823 9123.7598      0.1130
    2315   2317   80.0    0.1394 1790.7780      0.1420
    2315   2319   64.0    0.1497 1212.5186      0.1530
    2317   2318   89.8    0.1015 22272.4199      0.0971
    2319   2321  129.1    0.1483 397.1000      0.1420
    2321   2322   45.0    0.0925 178.4549      0.0971
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 2298 and 2301
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
************

The system seems to be well equilibrated.

Any thoughts?

Thanks in advance.

Best

Yasser

-- 
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernandez at chemie.uni-hamburg.de
office: Grindelallee 117, room 250c