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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
