An error about nonbonded interaction between particles during mdrun

Hello everyone
During mdrun for protein-ligand simulation ,which is 5000000 steps, I faced this error :

step 200500, will finish Fri Jun 10 03:53:47 2022
step 200600, will finish Fri Jun 10 03:53:56 2022
Step 200672, time 401.344 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000212, max 0.005807 (between atoms 5992 and 5993)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 30.9 0.1120 0.1127 0.1120
5992 5994 32.6 0.1120 0.1126 0.1120

Step 200674, time 401.348 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000168, max 0.004582 (between atoms 5992 and 5993)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 30.8 0.1120 0.1115 0.1120
5992 5994 31.7 0.1120 0.1115 0.1120

Step 200676, time 401.352 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000251, max 0.006853 (between atoms 5992 and 5994)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 34.1 0.1120 0.1127 0.1120
5992 5994 32.7 0.1120 0.1128 0.1120

Step 200678, time 401.356 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000196, max 0.005210 (between atoms 5992 and 5993)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 35.2 0.1120 0.1114 0.1120
5992 5994 35.2 0.1121 0.1114 0.1120

Step 200680, time 401.36 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000270, max 0.007748 (between atoms 5992 and 5994)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 37.0 0.1120 0.1127 0.1120
5992 5994 33.0 0.1120 0.1129 0.1120

Step 200682, time 401.364 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000213, max 0.005959 (between atoms 5992 and 5994)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 35.6 0.1121 0.1114 0.1120
5992 5994 32.6 0.1121 0.1113 0.1120

Step 200684, time 401.368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000344, max 0.009468 (between atoms 5992 and 5994)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 39.4 0.1120 0.1130 0.1120
5992 5994 35.9 0.1120 0.1131 0.1120

Step 200685, time 401.37 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000025, max 0.000721 (between atoms 5992 and 5993)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 32.1 0.1130 0.1121 0.1120

Step 200686, time 401.372 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000322, max 0.009066 (between atoms 5992 and 5994)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 39.4 0.1121 0.1111 0.1120
5992 5994 34.9 0.1121 0.1110 0.1120

Step 200688, time 401.376 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000826, max 0.023186 (between atoms 5992 and 5993)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 51.6 0.1120 0.1146 0.1120
5992 5994 56.7 0.1120 0.1142 0.1120

Step 200689, time 401.378 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000065, max 0.001803 (between atoms 5992 and 5994)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 46.7 0.1146 0.1122 0.1120
5992 5994 48.2 0.1142 0.1122 0.1120

Step 200692, time 401.384 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000699, max 0.018464 (between atoms 5992 and 5994)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 49.8 0.1122 0.1140 0.1120
5992 5994 50.1 0.1122 0.1141 0.1120

Step 200693, time 401.386 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000640, max 0.017301 (between atoms 5992 and 5993)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 61.1 0.1140 0.1101 0.1120
5992 5994 66.4 0.1141 0.1102 0.1120

Step 200695, time 401.39 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000115, max 0.003235 (between atoms 5992 and 5993)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 38.7 0.1119 0.1124 0.1120
5992 5994 43.6 0.1119 0.1123 0.1120

Step 200696, time 401.392 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001404, max 0.040276 (between atoms 5992 and 5993)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 58.7 0.1124 0.1165 0.1120
5992 5994 68.7 0.1123 0.1157 0.1120

Step 200697, time 401.394 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001368, max 0.040360 (between atoms 5992 and 5993)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 90.0 0.1165 0.1075 0.1120
5992 5994 90.0 0.1157 0.1154 0.1120

Step 200698, time 401.396 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.095646, max 2.532089 (between atoms 5992 and 5994)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5992 5993 90.0 0.1075 0.3059 0.1120
5992 5994 90.0 0.1154 0.3956 0.1120
5995 5996 90.0 0.1120 0.3114 0.1120
Wrote pdb files with previous and current coordinates

Step 200699, time 401.398 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 14075345.000000, max 519997952.000000 (between atoms 5992 and 5994)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4917 4918 38.3 0.1090 4887684.5000 0.1090
4919 4920 32.7 0.1090 0.1090 0.1090
5992 5993 90.0 0.3059 0.1159 0.1120
5992 5994 53.4 0.3956 58239768.0000 0.1120
5995 5996 90.0 0.3114 1.2561 0.1120
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 5986 and 5994
at distance 58239768.000 which is larger than the table limit 2.320 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 force field that I used was gromos54a7 and minimization results are in the picture that I upload.
I will be appreciate if you help me tackle this problem.
Capture