dear gmx-users, i am getting the following error message while running production md (mpirun)......
Step 102, time 0.204 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 122.760095, max 2890.435059 (between atoms 5092 and 5090) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5079 5069 30.7 0.1532 0.1888 0.1522 5081 5079 79.8 0.1056 0.2608 0.1335 5080 5079 39.1 0.1237 0.1673 0.1229 5083 5081 79.7 0.1459 0.8597 0.1449 5082 5081 78.7 0.1016 0.1856 0.1010 5098 5083 78.5 0.1532 0.7685 0.1522 5085 5083 85.9 0.1537 1.9840 0.1526 5084 5083 70.4 0.1097 0.4235 0.1090 5088 5085 83.6 0.1536 2.4114 0.1526 5087 5085 85.9 0.1098 1.5565 0.1090 5086 5085 87.3 0.1099 1.2617 0.1090 5088 5094 88.6 0.1535 3.0328 0.1526 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 5093 and 5094 at distance 6.570 which is larger than the 1-4 table size 2.200 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 Warning: 1-4 interaction between 5091 and 5094 at distance 2.444 which is larger than the 1-4 table size 2.200 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 Fatal error: 1 particles communicated to PME node 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. any suggestion to get rid of this problem........ Ansuman Biswas Physics Department Indian Institute of Science Bangalore India -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists