Usually this means your "doubling" didn't allow for the required space between atoms at the boundaries. It is usually less painful for a solute+solvent system to go back to your solute-only coordinate file, put a box around it with editconf, replicate that with genconf, and only then get solvent involved with genbox.
Mark On Tue, Jun 25, 2013 at 5:25 PM, Kieu Thu Nguyen <kieuthu2...@gmail.com> wrote: > Dear users, > > How can i fix the system structure while minimizing energy ? I made a > larger system by double a small system. But i can not continue simulation > because the system crashed after EM. Although the small system was > equilibrated well before doubling. > > Thankful for any help and regards, > > Thu > -- > 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 -- 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
