[gmx-users] POSITION RESTRAIN ERROR

[MUSYOKA THOMMAS]

Dear Users,
I am running Protein-Ligand MD simulations. Whenever, i get to do the
Position restrain run of both my protein and ligand, i get this error;
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Protein in water'
50000 steps,    100.0 ps.
step 0
Step 8, time 0.016 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.080448, max 2.357673 (between atoms 2458 and 2457)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2458   2457   87.8    0.1141   0.3828      0.1140
   2459   2458   86.7    0.1431   0.3658      0.1430
   2461   2459   53.2    0.1340   0.1619      0.1340
   2460   2459   53.2    0.1341   0.1672      0.1340
Wrote pdb files with previous and current coordinates

Step 9, time 0.018 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.823957, max 98.964455 (between atoms 2458 and 2457)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2458   2457   78.0    0.3828  11.3959      0.1140
   2459   2458  101.2    0.3658  10.0612      0.1430
   2461   2459   85.5    0.1619   2.9966      0.1340
   2460   2459  119.1    0.1672   4.7966      0.1340
   2466   2460  141.3    0.1532   3.1407      0.1340
   2467   2474  120.0    0.1132   0.6682      0.1120
   2476   2474   39.0    0.1343   0.1077      0.1340
   2467   2468  108.0    0.1483   0.7201      0.1470
   2469   2468   33.9    0.1532   0.1473      0.1530
   2464   2466  114.5    0.1455   0.5169      0.1390
   2464   2465   44.6    0.1895   0.2021      0.1870
   2462   2461  112.9    0.1640   5.8194      0.1400
   2464   2462   87.1    0.1438   2.1170      0.1390
   2463   2462   43.8    0.1125   1.2153      0.1090

Step 9, time 0.018 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.650577, max 22.438158 (between atoms 2466 and 2460)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2466   2464  114.5    0.1455   0.5169      0.1390
   2465   2464   44.6    0.1895   0.2021      0.1870
   2464   2462   87.1    0.1438   2.1170      0.1390
   2462   2463   43.8    0.1125   1.2153      0.1090
   2462   2461  112.9    0.1640   5.8194      0.1400
   2459   2461   85.5    0.1619   2.9966      0.1340
   2459   2460  119.1    0.1672   4.7966      0.1340
   2459   2458  101.2    0.3658  10.0612      0.1430
   2458   2457   78.0    0.3828  11.3959      0.1140
   2466   2460  141.3    0.1532   3.1407      0.1340
   2474   2467  120.0    0.1132   0.6680      0.1120
   2468   2467  108.0    0.1483   0.7200      0.1470
   2469   2468   33.9    0.1532   0.1473      0.1530
   2476   2474   39.4    0.1343   0.1089      0.1340
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 2457 and 2460 at distance 14.992 which is
larger than the 1-4 table size 2.400 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

Will be glad to learn how to go about it?

Kind regards