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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.