Hi all, I am trying to simulate a small organic molecule (42 atoms with 18 hydrogens among them) in water (SPCE). The force field was generated with X2TOP utility using GROMOS96 force field. All bonds, pairs, angles, dihedrals, etc are OK and the system runs OK but sometimes it craches producing several PDB files and CORE files. The message in the standart output is:
t = 122.523 ps: Water molecule starting at atom 2497 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 62 and 80 at distance 2653175545629928960.000 which is larger than the 1-4 table size 2.450 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 t = 122.524 ps: Water molecule starting at atom 1009 can not be settled. Check for bad contacts and/or reduce the timestep. t = 122.524 ps: Water molecule starting at atom 1693 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates The timestep is 1fs, the temperature varies from 25C up to 70C, barostat is turned on. If I reduce the timestep to 0.25fs, the problem does not appear fortunately but I would like to keep it equal to 1fs. I am sure the problem is with an organic molecule because it doesn't appear with SPCE water only. In the organic molecule nexcl=3 and all angles are defined well. Trying LINCS instead, I got a big number of warnings (>1000). What can be wrong with my force field (generated by X2TOP) else ? Thanks in advance. -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
