[gmx-users] Check for bad contacts and/or reduce the timestep

[pragna lakshmi]

Hi,
     I am trying to run protein-ligand complex simulation. At the final MD
run step it is showing the following error. Can anybody tell me the
solution for this error?

Step 105692, time 211.384 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002880, max 0.071917 (between atoms 2097 and 2095)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2098   2099   38.6    0.1330   0.1371      0.1330
   2097   2098   45.2    0.1330   0.1370      0.1330
.
.
.
.
Step 226039, time 452.078 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 42.444550, max 1059.016235 (between atoms 2098 and 2099)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2095   2094   31.6    0.1441  10.5310      0.1250
   2113   2114   40.8    0.1471   0.1950      0.1470
   2117   2112   36.4    0.1521   0.1902      0.1520
   2111   2113   81.7    0.1535   0.2949      0.1520
   2111   2112   83.9    0.1534   0.2900      0.1520
   2111   2110  113.2    0.1833   0.8261      0.1780
   2109   2110   43.8    0.2063  11.5418      0.1750
   2107   2109   38.3    0.1516  11.2487      0.1390
   2107   2108  103.0    0.1581  11.5450      0.1530
   2106   2107   77.4    0.1333  30.0780      0.1530
   2104   2105  140.0    0.1080   2.2354      0.1000
   2102   2104   34.2    0.1426  16.8737      0.1430
   2102   2103   89.9    0.1637  15.4076      0.1530
   2101   2106  142.0    0.2077  63.6808      0.1530
   2101   2102  132.5    0.1659  62.8960      0.1530
   2101   2099  174.7    0.5646 127.3807      0.1390
   2099   2100  160.1    0.5219 101.4140      0.1230
   2106   2098  166.3    0.2022  76.2729      0.1480
   2098   2099  174.8    0.6156 140.9822      0.1330
   2097   2109  149.5    0.1057  36.9859      0.1330
   2097   2098  159.4    0.2818  84.7773      0.1330
   2097   2095  164.8    0.1042  37.0501      0.1330
   2095   2096   70.7    0.1482   9.8470      0.1250
Wrote pdb files with previous and current coordinates
There were 4 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 2094 and 2098 at distance 44.117 which is
larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
.
.
.
.
   1416   1417   89.7    0.1530 705915256832.0000      0.1530
   1414   1416   90.4    0.1470 419510747136.0000      0.1470
   1414   1415   92.3    0.1000 45284384768.0000      0.1000
   1412   1414   89.5    0.1330 55051784192.0000      0.1330
   1412   1413  106.4    0.1230 13457604608.0000      0.1230
   1409   1411  119.2    0.1530 519590400.0000      0.1530
   1409   1410  107.4    0.1530 519590400.0000      0.1530
   1408   1412   99.1    0.1530 14933683200.0000      0.1530
   1408   1409   98.3    0.1530 4102264576.0000      0.1530
   1406   1408   98.5    0.1470 4076032256.0000      0.1470
   1406   1407  107.8    0.1000 606216384.0000      0.1000
   1404   1406  122.9    0.1330 606216384.0000      0.1330
   1404   1405   31.5    0.1230   0.1567      0.1230
   2120   2122  105.2    0.1473 84501076367114240.0000      0.1470
   2120   2121  105.8    0.1473 83934295302864896.0000      0.1470
   2118   2120   95.0    0.1349 219396825084329984.0000      0.1340
   2118   2119   96.0    0.1236 223179042004664320.0000      0.1230

t = 452.080 ps: Water molecule starting at atom 36608 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)


-- 
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin: 600006.
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