Thank Justin ! I made this rectangular box from merging two cubic boxes. And i carry out equilibrate this box. Do you mean that i should run NVT, and next step run NPT, to keep box shape fixed ?
Regards, ~Thu On Tue, Mar 19, 2013 at 3:39 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/18/13 1:36 PM, Kieu Thu Nguyen wrote: > >> Dear All, >> >> I want to equilibrate a rectangular box. But after running MD 60 ns, the >> system become to be a cubic box mostly. I do not want this happens. Can >> anyone tell me how to constrain the boxsize. In that case, the boxsize has >> fluctuations but remains the same box-type. >> >> > If the box shape changes drastically, that usually indicates instability > in the system. A stable simulation will preserve the original unit cell > shape. There is no special way to constrain it to behave as you want it > to. NVT keeps the box dimensions fixed, but that doesn't seem to be what > you want. > > -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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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
