One trick I am working with right now, is to have - periodic boundary conditions only xy - remove the COM motion of the water and the graphite separately. The COM motion is now removed only in the xy direction, so they are free to move in z. - put the surface (your graphite) at coordinate 0 - enable a wall. For this wall you can specify an atom type which specifies its interaction with the rest of the system. Make a special wall atom type that only interacts with the graphite.
This way you have a system that's free to move its COM in z, but not in xy, and still stays stuck to a specific coordinate. Sander On 26 Oct 2010, at 13:26 , Bert wrote: > Dear gmx-users, > > It is known that if system have an absolute reference, the removal of > COM could lead to artifacts. However, for instance, when one water > slab adsorbs on a freezed, infinite graphite surface, the COM motion > is still free in x or y direction, and subsequently leads to net flows > during long time simulations. I wanna know if there is a solution for > this case. Any suggestions will be appreciated. > > Best regards, > Bert > -- > 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
