Dear users I am trying to make MD of a crystal structure of carborane. This molecule is a ridge cage of 12-vertex (C2B10H12). I have all the bonding and non-bonding parameter from amber and I am working with this condition, for LJ interaction using sigma and epsilon
[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 I am using compresibility of 5 × 10-6 bar-1, mimicking conditions of zero surface tension, I think for a solid is OK, Is not it? . I am a bit confusing, I am using LINCS constraints for all bonds but the simulation stop after 300ps with LINCS problems. "LINCS WARNING relative constraint deviation after LINCS " The simulation stop because the system is not well equilibrated. When I work without Domain Descomposition the dynamics is more stable, but when I use constraints equal none or Hbonds the dynamics it is stable. The question When have I to change the type of constrains? Thanks for help me with this problems Hernan ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- 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
