[gmx-users] Segmentation fault error during run

[Justin Lemkul]

On 1/18/17 4:57 AM, Yasser Almeida Hernández wrote:
> 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 physical instability argues otherwise, or suggests you have an unreliable 
topology.  As always, simplify matters and test everything before trying to make 
some behemoth, heterogeneous system.  Ligand alone in vacuum, protein-ligand in 
water, etc.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================