Hi,<div> 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?</div><div><br></div><div><div>Step 105692, time 211.384 (ps) LINCS WARNING</div>
<div>relative constraint deviation after LINCS:</div><div>rms 0.002880, max 0.071917 (between atoms 2097 and 2095)</div><div>bonds that rotated more than 30 degrees:</div><div> atom 1 atom 2 angle previous, current, constraint length</div>
<div> 2098 2099 38.6 0.1330 0.1371 0.1330</div><div> 2097 2098 45.2 0.1330 0.1370 0.1330</div><div>.</div><div>.</div><div>.</div><div>.</div><div><div>Step 226039, time 452.078 (ps) LINCS WARNING</div>
<div>relative constraint deviation after LINCS:</div><div>rms 42.444550, max 1059.016235 (between atoms 2098 and 2099)</div><div>bonds that rotated more than 30 degrees:</div><div> atom 1 atom 2 angle previous, current, constraint length</div>
<div> 2095 2094 31.6 0.1441 10.5310 0.1250</div><div> 2113 2114 40.8 0.1471 0.1950 0.1470</div><div> 2117 2112 36.4 0.1521 0.1902 0.1520</div><div> 2111 2113 81.7 0.1535 0.2949 0.1520</div>
<div> 2111 2112 83.9 0.1534 0.2900 0.1520</div><div> 2111 2110 113.2 0.1833 0.8261 0.1780</div><div> 2109 2110 43.8 0.2063 11.5418 0.1750</div><div> 2107 2109 38.3 0.1516 11.2487 0.1390</div>
<div> 2107 2108 103.0 0.1581 11.5450 0.1530</div><div> 2106 2107 77.4 0.1333 30.0780 0.1530</div><div> 2104 2105 140.0 0.1080 2.2354 0.1000</div><div> 2102 2104 34.2 0.1426 16.8737 0.1430</div>
<div> 2102 2103 89.9 0.1637 15.4076 0.1530</div><div> 2101 2106 142.0 0.2077 63.6808 0.1530</div><div> 2101 2102 132.5 0.1659 62.8960 0.1530</div><div> 2101 2099 174.7 0.5646 127.3807 0.1390</div>
<div> 2099 2100 160.1 0.5219 101.4140 0.1230</div><div> 2106 2098 166.3 0.2022 76.2729 0.1480</div><div> 2098 2099 174.8 0.6156 140.9822 0.1330</div><div> 2097 2109 149.5 0.1057 36.9859 0.1330</div>
<div> 2097 2098 159.4 0.2818 84.7773 0.1330</div><div> 2097 2095 164.8 0.1042 37.0501 0.1330</div><div> 2095 2096 70.7 0.1482 9.8470 0.1250</div><div>Wrote pdb files with previous and current coordinates</div>
<div>There were 4 inconsistent shifts. Check your topology</div><div>Warning: 1-4 interaction between 2094 and 2098 at distance 44.117 which is larger than the 1-4 table size 2.000 nm</div><div>These are ignored for the rest of the simulation</div>
<div>This usually means your system is exploding,</div><div>if not, you should increase table-extension in your mdp file</div><div>or with user tables increase the table size</div></div><div>.</div><div>.</div><div>.</div>
<div>.</div><div><div> 1416 1417 89.7 0.1530 705915256832.0000 0.1530</div><div> 1414 1416 90.4 0.1470 419510747136.0000 0.1470</div><div> 1414 1415 92.3 0.1000 45284384768.0000 0.1000</div>
<div> 1412 1414 89.5 0.1330 55051784192.0000 0.1330</div><div> 1412 1413 106.4 0.1230 13457604608.0000 0.1230</div><div> 1409 1411 119.2 0.1530 519590400.0000 0.1530</div><div> 1409 1410 107.4 0.1530 519590400.0000 0.1530</div>
<div> 1408 1412 99.1 0.1530 14933683200.0000 0.1530</div><div> 1408 1409 98.3 0.1530 4102264576.0000 0.1530</div><div> 1406 1408 98.5 0.1470 4076032256.0000 0.1470</div><div> 1406 1407 107.8 0.1000 606216384.0000 0.1000</div>
<div> 1404 1406 122.9 0.1330 606216384.0000 0.1330</div><div> 1404 1405 31.5 0.1230 0.1567 0.1230</div><div> 2120 2122 105.2 0.1473 84501076367114240.0000 0.1470</div><div> 2120 2121 105.8 0.1473 83934295302864896.0000 0.1470</div>
<div> 2118 2120 95.0 0.1349 219396825084329984.0000 0.1340</div><div> 2118 2119 96.0 0.1236 223179042004664320.0000 0.1230</div><div><br></div><div>t = 452.080 ps: Water molecule starting at atom 36608 can not be settled.</div>
<div>Check for bad contacts and/or reduce the timestep.</div><div>Wrote pdb files with previous and current coordinates</div><div>Segmentation fault (core dumped)</div></div><div><br></div><div><br></div>-- <br><div style="line-height:normal">
<span style="font-family:"Times New Roman","serif";font-size:12pt">T.Pragna Lakshmi,</span></div><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Junior Scientist,</span></div>
<div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt"><span style="font-family:"Times New Roman","serif";font-size:12pt">Vision Research Center,</span></span></div>
<div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Sankara Netralaya,</span></div><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Chennai,</span></div>
<div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">India.</span></div><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Pin: 600006.</span></div>
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