Hey : When increasing the system size like that, make sure that all molecules in the original box are whole (trjconv -pbc mol). Only then can you, e.g., use genconf to double the system.
Cheers, Tsjerk On Sat, Jun 15, 2013 at 1:49 PM, Justin Lemkul <[email protected]> wrote: > > > On 6/15/13 6:21 AM, Kieu Thu Nguyen wrote: > >> Dear users, >> >> I make a rectangle bilayer by doubling two equilibrated cubic boxes. But >> after minimizing, the system have been crashed. I do not understand why. I >> attach the em.mdp below >> >> > The list does not allow attachments. Either copy and paste or provide a > link to where the file can be downloaded. The .mdp file may or may not be > useful. You should carefully inspect the starting configuration for atomic > overlap, and then otherwise follow the instructions described here: > > http://www.gromacs.org/**Documentation/Terminology/** > Blowing_Up#Diagnosing_an_**Unstable_System<http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System> > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Tsjerk A. Wassenaar, Ph.D. -- 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
