Hi, Sure, that's what trjconv -pbc and -ur are used for. There's no way to ask mdrun to automatically do the particular operation you want.
Mark On Tue, May 29, 2018 at 3:21 PM Alex <alexanderwie...@gmail.com> wrote: > Hi Mark, > Thanks. > The problem is that only the slab shifts and water molecules stay x-y > centrally in the box. Similar to the picture in the link below: > https://drive.google.com/open?id=1TwkgpesJPfFUiqxhl9rXBU33dwWn-tyD > Regards, > Alex > > On Fri, May 25, 2018 at 5:30 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > mdrun suits itself because there's no way to guess how to keep everybody > > happy with the form of the output. > > > > You shouldn't need to care, but if you want to put the center of the box > > somewhere, editconf and trjconv do that. > > > > Mark > > > > On Thu, May 24, 2018 at 9:58 PM Alex <alexanderwie...@gmail.com> wrote: > > > > > Dear all, > > > I have system containing a solid slab and water molecules on top of it > > in a > > > rectangle box ( 6.67350 , 6.96840, 8.68584). I do not know why the > > whole > > > slab completely shift in the Y direction after minimization!? The shift > > > approximately is equal to the Y-cell size (6.96840). It might not be > > > critical issue due to presence of PBC, but at least is weird and not > good > > > looking. The pressures in XX, YY are similar in my knowledge. Would you > > > please let me know I can find the reason and how to fix it? > > > Thank you > > > Alex > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
