[gmx-users] Core dumped in NVT
Dallas Warren
dallas.warren at monash.edu
Wed May 2 01:14:50 CEST 2018
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
On 1 May 2018 at 22:06, Syed Azeem <syedazeemullah186 at gmail.com> wrote:
> Hey all,
>
> I'm trying to simulate a peptide-protein docked complex. I docked the
> peptide using pepATTRACT package. After analysis, I selected the best
> pose and tried to simulate. This yielded an error and got core dumped
> in NVT equilibriation.
>
> I'm using GROMOS 54a7 force field. The error is pasted below:
>
> GROMACS: gmx mdrun, VERSION 5.1.4
> Executable: /usr/local/gromacs/bin/gmx
> Data prefix: /usr/local/gromacs
> Command line:
> gmx mdrun -v -deffnm nvt
>
>
> Running on 1 node with total 2 cores, 4 logical cores
> Hardware detected:
> CPU info:
> Vendor: GenuineIntel
> Brand: Intel(R) Core(TM) i3-4030U CPU @ 1.90GHz
> SIMD instructions most likely to fit this hardware: AVX2_256
> SIMD instructions selected at GROMACS compile time: AVX2_256
>
> Reading file nvt.tpr, VERSION 5.1.4 (single precision)
> Changing nstlist from 10 to 25, rlist from 1.4 to 1.434
>
> Using 1 MPI thread
> Using 4 OpenMP threads
>
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.056487, max 0.946381 (between atoms 2400 and 2402)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> Wrote pdb files with previous and current coordinates
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.220257, max 3.677571 (between atoms 94 and 95)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 55 56 31.8 0.1015 0.0956 0.1000
> 55 57 52.1 0.2349 0.2349 0.1470
> 57 58 48.0 0.2224 0.2228 0.1530
> 57 65 89.8 0.2299 0.3183 0.1530
> 65 66 69.6 0.1477 0.2354 0.1230
> 65 67 83.7 0.1946 0.2569 0.1330
> 67 68 68.2 0.1047 0.1408 0.1000
> 67 69 50.9 0.2300 0.2789 0.1470
> 69 70 63.0 0.2227 0.3403 0.1530
> 69 82 67.3 0.2495 0.3697 0.1530
> 70 71 54.1 0.1729 0.2028 0.1530
> 71 72 36.8 0.1991 0.2163 0.1530
> 82 83 55.4 0.1253 0.1783 0.1230
> 82 84 63.5 0.2539 0.2903 0.1330
> 84 85 62.5 0.1027 0.1596 0.1000
> 84 86 62.5 0.2388 0.4224 0.1470
> 86 87 79.9 0.1946 0.1769 0.1530
> 86 90 93.5 0.2100 0.2881 0.1530
> 90 91 37.7 0.1291 0.3171 0.1230
> 92 93 151.5 0.1057 0.1022 0.1000
> 92 94 157.5 0.1820 0.2864 0.1470
> 95 96 171.9 0.1609 0.1718 0.1530
> 95 97 169.2 0.1610 0.1759 0.1530
> 98 99 155.3 0.1402 0.1854 0.1230
> 98 100 162.4 0.1610 0.2476 0.1330
> 2386 2388 169.4 0.1544 0.2630 0.1470
> 2388 2389 163.7 0.1629 0.3605 0.1530
> 2392 2394 159.8 0.1330 0.2451 0.1330
> 2394 2395 150.3 0.0977 0.1349 0.1000
> 2396 2400 156.7 0.1776 0.1941 0.1530
> 2397 2398 166.4 0.1396 0.0462 0.1430
> 2400 2401 133.5 0.1069 0.1620 0.1230
> 2402 2403 48.6 0.1129 0.1661 0.1000
> 2402 2404 102.9 0.2098 0.2774 0.1470
> 2404 2411 34.6 0.2530 0.4458 0.1530
> 2405 2406 170.9 0.1595 0.1029 0.1530
> 2411 2412 46.5 0.1265 0.0735 0.1230
> 2411 2413 63.4 0.1713 0.1585 0.1330
> 2413 2414 35.3 0.1044 0.1095 0.1000
> 2413 2415 52.2 0.1872 0.0940 0.1470
> 2420 2421 88.5 0.1262 0.0936 0.1230
> 2420 2422 95.5 0.1656 0.2391 0.1330
> 2422 2423 49.7 0.1164 0.1810 0.1000
> 2422 2424 57.5 0.2148 0.3306 0.1470
> 2424 2425 54.2 0.1857 0.1855 0.1530
> 2424 2430 45.8 0.1815 0.1585 0.1530
>
> Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#
>
> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
> Wrote pdb files with previous and current coordinates
> starting mdrun 'Protein in water'
> 250000 steps, 500.0 ps.
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 3.611257, max 94.899414 (between atoms 57 and 65)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 50 52 69.3 0.1533 0.0680 0.1470
> 52 53 32.5 0.1728 0.2443 0.1530
> 53 54 41.0 0.1367 0.2362 0.1230
> 53 55 115.4 0.1420 1.1222 0.1330
> 55 56 100.2 0.1015 1.1348 0.1000
> 55 57 160.7 0.2349 3.2040 0.1470
> 57 58 130.5 0.2224 3.9408 0.1530
> 57 65 159.2 0.2299 14.6726 0.1530
> 58 59 111.8 0.1708 0.5409 0.1530
> 65 66 168.4 0.1477 11.3585 0.1230
> 65 67 76.0 0.1946 9.0458 0.1330
> 67 68 76.4 0.1047 0.8620 0.1000
> 67 69 148.6 0.2300 1.2341 0.1470
> 69 70 145.4 0.2227 1.2258 0.1530
> 70 71 56.0 0.1729 7.6068 0.1530
> 71 72 149.4 0.1991 8.1804 0.1530
> 72 73 37.2 0.1707 1.4197 0.1470
> 73 74 161.0 0.1090 0.5447 0.1000
> 73 75 158.7 0.1593 0.4927 0.1340
> 75 76 36.8 0.1472 0.8323 0.1340
> 76 77 70.7 0.1078 0.0542 0.1000
> 76 78 72.6 0.1104 0.0537 0.1000
> 79 80 68.5 0.1076 0.1054 0.1000
> 79 81 71.1 0.1090 0.0503 0.1000
> 82 83 84.2 0.1253 0.6714 0.1230
> 82 84 170.1 0.2539 0.6172 0.1330
> 84 85 75.8 0.1027 0.2144 0.1000
> 84 86 33.9 0.2388 0.9835 0.1470
> 86 87 167.4 0.1946 0.5811 0.1530
> 86 90 172.0 0.2100 0.9876 0.1530
> 92 93 147.3 0.1057 1.1116 0.1000
> 92 94 174.7 0.1820 2.2207 0.1470
> 95 96 172.9 0.1609 1.5246 0.1530
> 95 97 174.6 0.1610 1.5279 0.1530
> 98 99 157.5 0.1402 1.4389 0.1230
> 98 100 175.1 0.1610 1.6162 0.1330
> 100 101 31.7 0.1177 0.6587 0.1000
> 102 103 36.4 0.1614 0.0426 0.1530
> 103 104 39.8 0.1256 0.1126 0.1230
> 1960 1962 52.6 0.1595 0.1904 0.1530
> 1962 1963 70.9 0.1255 0.1585 0.1230
> 1962 1964 117.0 0.1378 0.4309 0.1330
> 1964 1965 91.0 0.1013 0.6623 0.1000
> 1964 1966 88.7 0.1530 4.6647 0.1470
> 1966 1967 90.5 0.1584 4.7378 0.1530
> 1966 1968 92.1 0.1582 4.5849 0.1530
> 1968 1969 64.0 0.1258 0.0756 0.1230
> 1968 1970 48.0 0.1375 0.1256 0.1330
> 1970 1971 144.1 0.1005 0.0170 0.1000
> 2379 2384 102.6 0.1617 0.0874 0.1530
> 2384 2385 123.0 0.1331 0.1377 0.1230
> 2386 2388 165.0 0.1544 1.3676 0.1470
> 2388 2389 173.9 0.1629 1.7754 0.1530
> 2392 2394 174.2 0.1330 1.3378 0.1330
> 2394 2395 141.9 0.0977 0.6955 0.1000
> 2396 2400 171.6 0.1776 1.0980 0.1530
> 2397 2398 176.3 0.1396 0.3120 0.1430
> 2398 2399 33.9 0.1068 0.1391 0.1000
> 2400 2401 141.6 0.1069 0.6928 0.1230
> 2402 2403 80.0 0.1129 0.3776 0.1000
> 2402 2404 173.3 0.2098 0.6670 0.1470
> 2405 2406 166.0 0.1595 0.8982 0.1530
> 2408 2409 167.1 0.1029 0.1642 0.1000
> 2408 2410 88.3 0.1025 0.0811 0.1000
> 2411 2412 129.6 0.1265 0.3673 0.1230
> 2411 2413 131.9 0.1713 0.4275 0.1330
> 2413 2414 42.4 0.1044 0.1792 0.1000
> 2415 2416 151.1 0.1771 0.0791 0.1530
> 2415 2420 99.0 0.2292 0.0795 0.1530
> 2422 2423 116.2 0.1164 0.0794 0.1000
> 2422 2424 77.6 0.2148 0.0743 0.1470
> 2430 2431 48.7 0.1358 0.1051 0.1230
> 2430 2432 107.9 0.1577 0.0385 0.1330
>
> step 0: Water molecule starting at atom 8717 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#
>
> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#
> Wrote pdb files with previous and current coordinates
> step 0
>
> WARNING: Listed nonbonded interaction between particles 52 and 57
> at distance 4.202 which is larger than the table limit 2.434 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.
>
>
>
> WARNING: Listed nonbonded interaction between particles 1960 and 1966
> at distance 4.395 which is larger than the table limit 2.434 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.
>
>
>
> Step 1, time 0.002 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 445919.686545, max 10488755.000000 (between atoms 86 and 87)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 50 52 52.8 0.0680 0.1968 0.1470
> 52 53 88.5 0.2443 1.7395 0.1530
> 53 54 93.1 0.2362 1.3434 0.1230
> 55 57 120.2 3.2040 7.6036 0.1470
> 57 58 149.4 3.9408 5.9538 0.1530
> 58 59 80.4 0.5409 0.7978 0.1530
> 59 60 120.4 0.1913 0.1180 0.1530
> 60 61 30.8 0.0644 0.1465 0.1230
> 67 68 169.0 0.8620 2.2796 0.1000
> 67 69 95.5 1.2341 4.7829 0.1470
> 69 70 99.0 1.2258 1489450.5000 0.1530
> 69 82 88.6 1.3749 4.1414 0.1530
> 70 71 101.0 7.6068 1489447.7500 0.1530
> 71 72 34.2 8.1804 25.0648 0.1530
> 72 73 98.0 1.4197 4.3013 0.1470
> 73 74 112.9 0.5447 2.1504 0.1000
> 73 75 150.6 0.4927 3.5357 0.1340
> 75 76 177.5 0.8323 2.6786 0.1340
> 75 79 177.9 0.8048 2.6948 0.1340
> 76 77 39.5 0.0542 1.2053 0.1000
> 76 78 54.2 0.0537 1.2105 0.1000
> 79 81 37.8 0.0503 1.1745 0.1000
> 82 83 116.8 0.6714 12.4030 0.1230
> 82 84 75.8 0.6172 5.1618 0.1330
> 84 85 80.1 0.2144 3.3172 0.1000
> 84 86 158.8 0.9835 2.3111 0.1470
> 86 87 127.0 0.5811 1604779.6250 0.1530
> 86 90 131.9 0.9876 22.6362 0.1530
> 87 88 136.3 0.2633 1604777.6250 0.1530
> 87 89 134.5 0.2626 1604777.6250 0.1530
> 90 91 99.4 0.8835 18.4914 0.1230
> 90 92 101.2 1.7391 18.2325 0.1330
> 92 93 168.5 1.1116 2.4413 0.1000
> 92 94 151.9 2.2207 4.2493 0.1470
> 94 95 146.4 2.9677 197.0873 0.1530
> 94 98 94.5 2.9018 4.7508 0.1530
> 95 96 136.2 1.5246 197.0424 0.1530
> 95 97 135.8 1.5279 196.5028 0.1530
> 98 99 70.1 1.4389 4.7830 0.1230
> 98 100 177.4 1.6162 3.9290 0.1330
> 100 101 161.8 0.6587 2.4983 0.1000
> 100 102 167.4 0.6994 2.0530 0.1470
> 102 103 32.3 0.0426 0.4770 0.1530
> 103 104 149.1 0.1126 0.2590 0.1230
> 103 105 121.0 0.1429 0.2252 0.1330
> 105 106 45.4 0.1047 0.1199 0.1000
> 105 107 40.7 0.1506 0.1856 0.1470
> 459 460 37.7 0.1004 0.1232 0.1000
> 459 461 118.0 0.1485 0.2399 0.1470
> 461 462 112.1 0.1539 0.2283 0.1530
> 461 464 54.6 0.1552 0.3513 0.1530
> 464 465 97.0 0.1236 0.3299 0.1230
> 464 466 132.1 0.1347 0.5037 0.1330
> 466 467 90.5 0.1001 0.8933 0.1000
> 466 468 75.7 0.1488 245.1382 0.1470
> 468 469 117.9 0.1535 245.6971 0.1530
> 468 473 68.4 0.1543 244.8664 0.1530
> 469 470 88.8 0.1532 2.0162 0.1530
> 470 471 88.9 0.1531 0.2683 0.1530
> 470 472 88.4 0.1530 0.2865 0.1530
> 473 474 67.6 0.1236 0.2658 0.1230
> 473 475 47.8 0.1340 0.2943 0.1330
> 475 477 37.8 0.1475 0.1543 0.1470
> 480 482 89.7 0.1330 0.3972 0.1330
> 482 483 89.9 0.1000 0.4255 0.1000
> 482 484 89.8 0.1000 0.3447 0.1000
> 874 875 64.1 0.1090 0.1118 0.1090
> 876 877 90.0 0.1090 1.2724 0.1090
> 971 973 90.9 0.1330 0.1355 0.1330
> 973 974 89.8 0.1000 0.1655 0.1000
> 973 975 59.6 0.1470 0.2659 0.1470
> 975 976 45.4 0.1530 0.1641 0.1530
> 975 977 90.0 0.1530 0.2467 0.1530
> 1181 1183 32.3 0.1470 0.1820 0.1470
> 1183 1184 33.4 0.1530 0.1897 0.1530
> 1183 1186 87.1 0.1530 0.4631 0.1530
> 1186 1187 89.6 0.1230 2.0125 0.1230
> 1186 1188 87.0 0.1330 0.4667 0.1330
> 1188 1189 41.1 0.1000 0.1406 0.1000
> 1188 1190 41.6 0.1470 0.2042 0.1470
> 1217 1219 49.4 0.1470 0.2306 0.1470
> 1219 1220 48.2 0.1530 0.2333 0.1530
> 1219 1221 69.1 0.1530 0.1597 0.1530
> 1221 1222 71.5 0.1230 0.1676 0.1230
> 1221 1223 84.2 0.1330 0.6300 0.1330
> 1223 1224 83.5 0.1000 0.4255 0.1000
> 1223 1225 87.9 0.1470 2.2220 0.1470
> 1225 1226 83.0 0.1530 238.0161 0.1530
> 1225 1227 87.2 0.1530 2.0415 0.1530
> 1227 1228 79.3 0.1230 0.3599 0.1230
> 1227 1229 80.9 0.1330 0.4564 0.1330
> 1229 1230 77.4 0.1000 0.1608 0.1000
> 1229 1231 71.1 0.1470 0.2788 0.1470
> 1231 1232 30.6 0.1530 0.1813 0.1530
> 1231 1244 31.0 0.1530 0.1832 0.1530
> 1305 1307 47.4 0.1424 0.2134 0.1470
> 1307 1308 42.4 0.1533 0.2194 0.1530
> 1307 1315 88.2 0.1598 1.0322 0.1530
> 1315 1316 89.2 0.1248 0.9244 0.1230
> 1315 1317 87.2 0.1372 1.0287 0.1330
> 1317 1318 48.8 0.1008 0.1460 0.1000
> 1386 1388 44.9 0.1330 0.2007 0.1330
> 1388 1389 47.7 0.1000 0.1542 0.1000
> 1388 1390 82.6 0.1470 0.3387 0.1470
> 1390 1391 82.4 0.1530 0.2848 0.1530
> 1390 1403 82.4 0.1530 0.5333 0.1530
> 1391 1392 46.6 0.1530 0.2266 0.1530
> 1403 1404 81.7 0.1230 0.3695 0.1230
> 1403 1405 85.7 0.1330 1.7081 0.1330
> 1405 1406 87.3 0.1000 1.1905 0.1000
> 1405 1407 84.7 0.1470 199.9464 0.1470
> 1407 1408 125.1 0.1530 199.2922 0.1530
> 1407 1413 117.6 0.1530 200.0835 0.1530
> 1408 1409 89.9 0.1530 0.7903 0.1530
> 1409 1410 81.0 0.1530 0.0783 0.1530
> 1413 1414 82.5 0.1230 0.4086 0.1230
> 1413 1415 83.7 0.1330 0.5814 0.1330
> 1415 1416 80.2 0.1000 0.1747 0.1000
> 1415 1417 83.3 0.1470 0.2733 0.1470
> 1417 1418 45.6 0.1530 0.2203 0.1530
> 1518 1519 90.2 0.1530 1.0253 0.1530
> 1519 1520 89.9 0.1530 0.9727 0.1530
> 1520 1521 90.7 0.1530 0.3051 0.1530
> 1905 1910 75.8 0.1530 0.0979 0.1530
> 1910 1911 89.0 0.1230 0.1156 0.1230
> 1910 1912 89.3 0.1330 0.4959 0.1330
> 1912 1913 89.8 0.1000 0.4425 0.1000
> 1912 1914 89.9 0.1470 0.5036 0.1470
> 1941 1942 89.5 0.1250 0.1724 0.1250
> 1948 1956 30.7 0.1602 0.2005 0.1530
> 1956 1957 35.2 0.1324 0.1723 0.1230
> 1956 1958 37.0 0.1318 0.1608 0.1330
> 1958 1959 62.2 0.1024 0.1575 0.1000
> 1958 1960 79.2 0.0993 0.4421 0.1470
> 1960 1961 86.3 0.1074 0.4064 0.1530
> 1960 1962 97.7 0.1904 1.2281 0.1530
> 1962 1963 93.7 0.1585 1.1917 0.1230
> 1962 1964 100.0 0.4309 257.3985 0.1330
> 1964 1965 102.9 0.6623 257.9689 0.1000
> 1964 1966 55.0 4.6647 247.7282 0.1470
> 1966 1967 36.0 4.7378 3.8114 0.1530
> 1968 1969 42.0 0.0756 2.0450 0.1230
> 1968 1970 92.4 0.1256 2.3649 0.1330
> 1970 1971 114.5 0.0170 0.0411 0.1000
> 1970 1972 66.6 0.1409 0.2432 0.1470
> 1997 1999 36.8 0.1471 0.1973 0.1470
> 1999 2000 37.9 0.1531 0.2066 0.1530
> 1999 2012 75.2 0.1532 0.2838 0.1530
> 2012 2013 76.3 0.1232 0.2615 0.1230
> 2012 2014 91.6 0.1334 4.4373 0.1330
> 2014 2015 89.9 0.1001 4.0712 0.1000
> 2014 2016 88.7 0.1475 4.5518 0.1470
> 2016 2017 90.6 0.1534 0.8688 0.1530
> 2016 2021 98.9 0.1537 0.7395 0.1530
> 2017 2018 93.2 0.1532 0.0531 0.1530
> 2021 2022 90.7 0.1233 0.1515 0.1230
> 2021 2023 65.2 0.1335 0.1229 0.1330
> 2023 2024 118.9 0.1002 0.0514 0.1000
> 2026 2029 90.0 0.1530 0.4266 0.1530
> 2034 2035 91.3 0.1530 0.4582 0.1530
> 2035 2036 89.6 0.1530 1.5115 0.1530
> 2036 2037 90.3 0.1530 1.2850 0.1530
> 2036 2038 90.2 0.1530 1.1447 0.1530
> 2377 2378 79.3 0.1023 0.0471 0.1000
> 2377 2379 57.8 0.1642 0.8357 0.1470
> 2379 2380 149.9 0.1616 0.7097 0.1530
> 2379 2384 162.6 0.0874 3.0653 0.1530
> 2380 2381 69.3 0.1503 0.2580 0.1430
> 2380 2383 70.4 0.1603 0.2605 0.1530
> 2381 2382 40.8 0.1008 0.1274 0.1000
> 2384 2385 157.3 0.1377 2.7199 0.1230
> 2384 2386 88.0 0.6749 5.7265 0.1330
> 2386 2387 175.1 0.5848 5.8374 0.1000
> 2386 2388 66.7 1.3676 2.4789 0.1470
> 2388 2389 145.8 1.7754 100.5195 0.1530
> 2388 2392 140.1 2.2155 7.9392 0.1530
> 2389 2390 154.9 1.0664 94.0989 0.1530
> 2389 2391 153.5 1.0644 94.1759 0.1530
> 2392 2393 119.2 1.1427 2.4289 0.1230
> 2392 2394 153.6 1.3378 4.7865 0.1330
> 2394 2395 59.0 0.6955 3.9258 0.1000
> 2394 2396 79.7 1.4536 0.8311 0.1470
> 2397 2398 173.2 0.3120 2.1241 0.1430
> 2398 2399 171.0 0.1391 0.8564 0.1000
> 2400 2401 58.5 0.6928 203.4008 0.1230
> 2400 2402 81.5 1.1983 225.7635 0.1330
> 2402 2403 81.0 0.3776 226.5243 0.1000
> 2402 2404 64.2 0.6670 265.1795 0.1470
> 2404 2405 70.5 1.0829 239.0391 0.1530
> 2404 2411 59.6 1.0115 239.2414 0.1530
> 2406 2407 175.1 0.8464 4.5223 0.1230
> 2406 2408 176.0 0.8165 4.7410 0.1330
> 2408 2409 163.4 0.1642 1.8649 0.1000
> 2408 2410 178.5 0.0811 1.8959 0.1000
> 2411 2412 156.9 0.3673 2.5776 0.1230
> 2411 2413 152.0 0.4275 2.8883 0.1330
> 2413 2414 111.3 0.1792 1.0293 0.1000
> 2413 2415 138.5 0.4719 0.9863 0.1470
> 2415 2416 153.1 0.0791 0.4251 0.1530
> 2415 2420 108.1 0.0795 0.5557 0.1530
> 2417 2418 33.7 0.1625 0.1585 0.1830
> 2420 2421 46.9 0.1893 0.1690 0.1230
> 2420 2422 45.4 0.3405 0.1951 0.1330
> 2422 2423 48.9 0.0794 0.0796 0.1000
> 2422 2424 81.9 0.0743 0.2502 0.1470
> 2424 2425 34.0 0.2998 0.1694 0.1530
> 2424 2430 52.4 0.2960 0.2009 0.1530
> 2430 2431 44.6 0.1051 0.1228 0.1230
> 2430 2432 52.0 0.0385 0.1634 0.1330
> 2432 2433 35.3 0.1378 0.1055 0.1000
>
> step 1: Water molecule starting at atom 10019 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Segmentation fault (core dumped)
>
> Please help me sort out this issue.
>
> Best,
> Azeem
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