Hi, You can't do any kind of dynamic updating of groups used for eg pulling. If you really need what you describe, then your only current option is to stop the simulation, run gmx select to generate new index groups and restart it. But I would consider alternatives, such as pushing (some of) the reservoir with the pull code.
Mark On Mon, 27 Feb 2017 13:40 Rana Ali <ranadeepu2...@gmail.com> wrote: > Dear GROMACS users, > I am working on 'Desalination process with CNT based membranes', where I > want to apply pressure gradient across CNT channel. I have fixed CNT > channel in z direction. This CNT channel is connected with NaCl solution > reservoir at top and fresh water reservoir at bottom. Now I want to apply a > constant force (in z direction) to the oxygen atoms of a subset of water > molecules in layers of 0.2nm thick, located at both end of simulation box. > Also, list of molecules in the subset is required to be updated in each at > 10 ps, which is different from time step. > However, I don't know how to define the sublayers in the simulation, like > group of oxygen atoms with z>3.0 and also I am unaware how to list of > molecules can be updated. It would be very kind if anyone can help me to > overcome this problem ? > With Thanks in Advance. > Pooja > -- > 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.
