I once constructed a solid hydrophilic wall by applying large constraints on an equilibrated slab of spce water. Just construct a simulation box of the size of the wall needed (don't make it too thin), equilibrate it, use genrestr in all 3 dimensions to construct a restraints file, and then genconf to place it in the final simulation box (after matching box sizes, etc). It worked pretty well for me.
On Tue, Dec 4, 2012 at 3:31 AM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > > Dear All users > > > > Can i construct a solid wall in gromacs? > > > > -- > > Sincerely > > > > Ali Alizadeh > > > Yes, you can. Atom-by-atom, until your castle is ready. > > > If you start with 1-atom unit cell, you can then > > genconf -f unitcell.gro -o wall.gro -nbox $many $many $many > > Afterwards, the only challenge is to place this wall correctly into > your [final] box. > > > Dr. Vitaly V. Chaban > MEMPHYS - Center for Biomembrane Physics > Department of Physics, Chemistry and Pharmacy > University of Southern Denmark > Campusvej 55, 5230 Odense M, Denmark > -- > 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 > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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